Alicia Calvo-Villamañán

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

Extremely grateful to everyone involved in the project.

Check it out!! 👇🏻👇🏻

With @saramitri.bsky.social, @sonjalehtinen.bsky.social and L. Lehmann we’ve launched the UNIL Center for Theory in Ecology and Evolution @unil.bsky.social🇨🇭

To kick things off, we’re offering short visiting fellowships for theorists in ecology & evolution. Apply & pls RP 😀

tinyurl.com/2wem36zz

Excited to share our latest work! 📝

We measured the fitness effect of 136 AMR genes and found that many are neutral or even beneficial without selection. 🤯🧬

Oxygen availability can flip their fitness and our stochastic model indicates that oxygen fluctuations help maintain them.

Learn more 👇🏼

Muchas gracias Pablo :)

I’m very happy to have joined the Evolutionary Biology lab in @gimminstitute.bsky.social as a postdoc, headed by @isabelgordo.bsky.social. After 10 years living abroad, I am finally back home! 2.6km away from where I grew up, to be exact! Here is to new adventures and amazing science by the ocean! 🥳

➡️ 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? 🤔

🧵👇

🔬 New work from the Mazel Lab engineers programmable conjugative plasmids to selectively target MDR bacteria and the resistance plasmid pOXA-48, blocking its spread in complex communities.

✍️ @amazeld.bsky.social & coll. @pasteur.fr
📖 shorturl.at/GZdJu

#MicroSky #AntibioticResistance #Conjugation

Thank you Pedro for leading this project so well!! It was super fun to be a part of it and a great pleasure to work with you 🥰

Amazing piece of work I had the great luck to be a part of!

Two cartoon images of children with plasmids for faces about to fight. Commentators are saying "Plasmid-borne CRISPR-Cas systems provide significant defensive benefits" and "Yes, but toxin-antitoxin systems on competitor plasmids constrain the offensive CRISPR-Cas benefit"

Out now in @plosbiology.org : our big joint effort on the role of #CRISPR in plasmid competition. Read on for a really fun (I’m biased ok) analysis of how a defence system has new selective pressures when it’s mobile
journals.plos.org/plosbiology/... 1/6

New pre-print with @wtmatlock.bsky.social!!!
www.biorxiv.org/content/10.6...
What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

Plasmid mutation rates scale with copy number | PNAS Plasmids are extrachromosomal DNA molecules that spread by horizontal transfer and shape bacterial evolution. Plasmids are typically present at mul...

New paper out in PNAS!!! 🎉

Do more plasmid copies mean faster evolution?

🧵 Dive into the story

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

I would like to particularly thank the PBE lab and @sanmillan.bsky.social for fostering a space where one can fall in love with these tiny molecules of DNA, explore science freely and grow into a mature scientist, from the very beginning. Os voy a echar a todxs mucho de menos.

Today is my last day working in the PBE lab @cnb-csic.bsky.social. Goodbyes are always bittersweet. These walls have seen me grow a lot as a scientist and a person, and I have all these lovely people to thank for it. I will carry you with me to my next adventure 🥰

Engineered living glues secrete therapeutic proteins for treatment of inflammatory bowel disease - Nature Biotechnology Engineered bacteria sense gut bleeding and secrete repair materials.

#NatMicroPicks

E. coli can be engineered to secrete a glue consisting of an adhesive protein and a healing factor, inducible in response to gastrointestinal bleeding, to treat colitis in a mouse model

@natbiotech.nature.com

www.nature.com/articles/s41...

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

#NatMicroPicks Baby-to-baby strain transmission shapes the developing gut microbiome - out now in Nature! 👶🦠👶

#microsky #microbiome @nature.com @cibiocm.bsky.social

www.nature.com/articles/s41...

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...

Bacteriophages are normally classified as either virulent or temperate. Reality is, of course, more complicated!
Here we show many bacterial isolates contain non-temperate phages that can persist through restreaking.
Thanks to all co-authors for such a great collaboration!

An excel spreadsheet with each cell filled with the word Gloria

Congrats David!!! So well deserved :)

The EMBO Gold Medal 2025 was awarded to Tanmay Bharat and David Bikard: https://www.embo.org/press-releases/embo-gold-medal-2025-awarded-to-tanmay-bharat-and-david-bikard/ 🧪

At #CellBio2025, the EMBO Gold Medal was handed over to David Bikard in recognition of his pioneering work on #GeneEditing.

On the plane after a fantastic few days in Liverpool at #MicroEvo25 organised by the @microbiologysociety.org. The science, the people, and the city were all way above expectations. I’m definitely coming back. Had an absolute blast!

Very happy to be at #microevo25 in Liverpool! Here’s to two days of micro-awesomeness and Beatles’ references!

Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti

Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5

An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

#microsky #phagesky CRISPR-cas galore

www.nature.com/articles/s41...

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...

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...

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 ...

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

New paper online at @nature.com from co-leads @erinedoherty.bsky.social + @benadler.bsky.social !

🔬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