Alicia Calvo-Villamañán
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aliciapcv.bsky.social
Alicia Calvo-Villamañán
@aliciapcv.bsky.social
| CRISPR, Plasmid Biology, Bacterial EcoEvo & AMR | Sci-Illustrator |

@embo.org postdoctoral fellow, San-Millán lab @cnb-csic.bsky.social 🇪🇸
Previously: PhD in Bikard Lab, @pasteur.fr 🇫🇷

| She/Her | From 🇪🇸 & 🇵🇹 | 💜
Pinned
This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...
rdcu.be
Reposted by Alicia Calvo-Villamañán
New paper with my (amazing) friend and mentor @jrpenades.bsky.social
Really looking forward to see what plasmid aficionados think of this one!!
With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others
www.cell.com/cell-reports...
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
www.cell.com
October 22, 2025 at 1:12 PM
Reposted by Alicia Calvo-Villamañán
New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky
Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage
Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...
www.biorxiv.org
October 9, 2025 at 10:07 AM
Reposted by Alicia Calvo-Villamañán
New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !
Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity.

Check out this work co-led with @benadler.bsky.social here:

www.nature.com/articles/s41...
A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature
Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.
www.nature.com
October 2, 2025 at 3:25 AM
Reposted by Alicia Calvo-Villamañán
🔬PPU 2025 Call for Candidates - Discover the PhD projects

Today's featured projects: 4 Cell Biology & Infection projects and 2 Parasites & Insect Vectors projects

🗓 Applications deadline: October 20, 2025
📍Program starts: October 2026

Discover all projects & apply now: bit.ly/4nlPz8x
September 30, 2025 at 4:09 PM
Reposted by Alicia Calvo-Villamañán
Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
August 27, 2025 at 1:37 PM
Reposted by Alicia Calvo-Villamañán
El grupo de Álvaro San Millán revela el coste de mantener la resistencia en enterobacterias

El trabajo traza un mapa funcional del plásmido pOXA-48, con potencial para guiar nuevas terapias contra resistencias

bit.ly/4p0fCmY

@sanmillan.bsky.social @aliciapcv.bsky.social @jorgesastred.bsky.social
Identifican el coste fisiológico de mantener la resistencia microbiana en enterobacterias - CNB
bit.ly
August 27, 2025 at 8:32 AM
Reposted by Alicia Calvo-Villamañán
Have you ever wondered what increasing environmental stress will do to microbial communities?

In our new preprint, @martinadalbello.bsky.social, Jeff Gore and I studied the impact of salinity on microbial community composition and function. 🧵 (1/5)
www.biorxiv.org/content/10.1...
Microbial communities demonstrate robustness in stressful environments due to predictable composition shifts
Environmental stress reduces species growth rates, but its impact on the function of microbial communities is less clear. Here, we experimentally demonstrate that increasing salinity stress shifts com...
www.biorxiv.org
August 25, 2025 at 2:33 PM
Reposted by Alicia Calvo-Villamañán
#NatMicroPicks

AI Designs Next-Gen Antibiotics! 💊🤖

Generative deep learning and genetic algorithms created structurally novel antibiotics that effectively target drug-resistant bacteria, offering a powerful new tool to combat drug resistance.

#MicroSky #AMR

www.cell.com/cell/abstrac...
A generative deep learning approach to de novo antibiotic design
A generative AI platform is developed for de novo antibiotic design, yielding lead compounds with selective antibacterial activity, distinct mechanisms of action, and in vivo efficacy against multidru...
www.cell.com
August 22, 2025 at 1:41 PM
Reposted by Alicia Calvo-Villamañán
Reposted by Alicia Calvo-Villamañán
🚨🚨New paper out in @natcomms.nature.com!!

Come for the first large-scale analysis of plasmid copy number across species,
stay for one of the most intriguing results of my lab: universal scaling laws in plasmid biology! 📈🧬

👉 www.nature.com/articles/s41...
Universal rules govern plasmid copy number - Nature Communications
Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...
www.nature.com
July 2, 2025 at 11:08 AM
Reposted by Alicia Calvo-Villamañán
For those who love bacterial replicons, The ultimate review, from our lab, signed by the master of their evolution.
‪@val-meve.bsky.social‬ www.sciencedirect.com/science/arti...
Taming wild replicons: evolution and domestication of large extrachromosomal replicons
Bacterial genomes often contain extrachromosomal replicons (ERs), ranging from small, mobile plasmids to large, stably inherited elements, such as meg…
www.sciencedirect.com
August 20, 2025 at 10:28 AM
This work is finally published! 🥳🧬
Plasmids are associated with very variable fitness costs in their different bacterial hosts. But, what is the contribution of each of the plasmid-genes in these host-specific effects? Study led by
@jorgesastred.bsky.social, @sanmillan.bsky.social and myself! 1/14
Dissecting pOXA-48 fitness effects in clinical Enterobacterales using plasmid-wide CRISPRi screens
Nature Communications - This study investigates the effects of the carbapenem resistance plasmid pOXA-48 in clinical enterobacteria. Using CRISPRi screens, the authors revealed that the...
rdcu.be
August 20, 2025 at 1:25 PM
Reposted by Alicia Calvo-Villamañán
#NewResearch

Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals.

#MicroSky 🦠

www.nature.com/articles/s41...
Characterization of an amyloid-based antiphage defence system in Escherichia coli - Nature Microbiology
Prion-like proteins in Escherichia coli trigger an abortive infection mechanism in response to phage infection—a process similar to amyloid-mediated immune signalling in fungi and animals.
www.nature.com
August 15, 2025 at 2:53 PM
Very happy to be a (small) part of this story!
The role of plasmid-encoded ISs in the acceleration of AMR evolution, through inactivation of different bacterial genes.
New paper out! 🔈🔈📣📣

Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation.

Combining experimental and computational approaches, we unveil how two of the most prevalent bacterial MGE accelerate the evolution of AMR. 🧵👇🏻

www.biorxiv.org/content/10.1...
Plasmids promote antimicrobial resistance through Insertion Sequence-mediated gene inactivation
Antimicrobial Resistance (AMR) is a major threat to public health. Plasmids are mobile genetic elements that can rapidly spread across bacterial populations, promoting the dissemination of AMR genes i...
www.biorxiv.org
August 13, 2025 at 11:09 AM
Reposted by Alicia Calvo-Villamañán
White smoke, we have a new pope and also 16 new anti-phages systems in sedentary integrons (SCIs) !
In collaboration with the Rocha lab, we show in our new paper that cassettes of these large platforms encode many known anti-phage defenses, and uncovered 16 new ones.
www.science.org/doi/10.1126/...
Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems
Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing, and shuffling gene cassettes. While mobile integrons are well known for spreading antibiotic resistance genes, t...
www.science.org
May 9, 2025 at 11:41 AM
Reposted by Alicia Calvo-Villamañán
Mapping of DNA-binding sites for 139 E. coli transcription factors

and

A neural network that predicts binding energy from DNA sequence and can be used to design new binding sites

#NeuralNetworks #MachineLearning #Genomics
Predictive biophysical neural network modeling of a compendium of in vivo transcription factor DNA binding profiles for Escherichia coli - Nature Communications
The authors describe BoltzNet, a neural network that learns the energy of transcription factor (TF)-DNA binding from genomic data and can be used to design new binding sites. They report the in vivo mapping and BoltzNet modeling of 139 E. coli TFs.
bit.ly
June 2, 2025 at 3:17 PM
Reposted by Alicia Calvo-Villamañán
Hoy no te pierdas la charla de nuestra compañera, @aliciapcv.bsky.social, investigadora en el #CNB_CSIC en la X edición de @pintofscience.es

🕢19.45h
📍Mercado de San Leopoldo ( Distrito Tetuán, Madrid)

ℹ️👇
pintofscience.es/event/viajan...
May 19, 2025 at 2:26 PM
Reposted by Alicia Calvo-Villamañán
I *finally* get to share our work on plasmid competition– super proud to now have this on bioRxiv:

CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin-antitoxin activity when horizontally transferred

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

1/6 👇
May 12, 2025 at 5:11 AM
Reposted by Alicia Calvo-Villamañán
cool preprint from a few months back: www.biorxiv.org/content/10.1...

Really intriguing IS strategy to become fixed in plasmids, where the IS cuts up any plasmid that doesn't contain the insertion sequence
RNA-guided nucleases enable a gene drive of insertion sequences in plasmids
Mobile genetic elements (MGEs) and the interactions between them are a major source of evolutionary innovation. Insertion sequences, the simplest MGEs usually encoding only the necessary genes for tra...
www.biorxiv.org
May 12, 2025 at 9:36 AM
Today, we Portuguese around the globe celebrate #25deAbril, also known as the Carnation Revolution. As fights for Democracy go, this one is a particularly beautiful one. 25 de Abril sempre, fascismo nunca mais 🌹
April 25, 2025 at 12:44 PM
Reposted by Alicia Calvo-Villamañán
Preprint out! Bacteria w/ hyper-replicative filamentous phage lead to overnight emergence of cheater phages. Bacteria w/ both phages can outcompete wildtype, then rapidly lose phage via a phage Tragedy of the Commons
@shellyscrib.bsky.social @vscooper.micropopbio.org www.biorxiv.org/content/10.1...
Filamentous cheater phages drive bacterial and phage populations to lower fitness
Many bacteria carry phage genome(s) in their chromosome (i.e., prophage), and this intertwines the fitness of the bacterium and the phage. Most Pseudomonas aeruginosa strains carry filamentous phages ...
www.biorxiv.org
April 2, 2025 at 12:41 PM
Reposted by Alicia Calvo-Villamañán
New online! Interactions and evolutionary relationships among bacterial mobile genetic elements
Interactions and evolutionary relationships among bacterial mobile genetic elements
Nature Reviews Microbiology, Published online: 11 March 2025; doi:10.1038/s41579-025-01157-yIn this Review, Lang and colleagues present an overview of the current knowledge landscape regarding mobile genetic elements in bacteria, with a focus on their…
www.nature.com
March 11, 2025 at 1:14 PM
Reposted by Alicia Calvo-Villamañán
The Eligo team did it again! We just shared on biorxiv the work we did towards the development of a CRISPR-Cas therapy targeting Shiga Toxin producing E. coli (STEC). www.biorxiv.org/content/10.1...
www.biorxiv.org
March 4, 2025 at 12:31 PM