Rafael Peña-Miller
@penamiller.bsky.social
Scientist working somewhere around mathematical, computational and experimental microbiology
New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.
Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells
rdcu.be
Registration is open for MEEHubs 2026!
MEEhubs@meehubs.bsky.social · 6mo agoMEEHubs2026 registration and abstract submission is now online! 🚨🦠✨ Join us Aug 3 - 5, 2026 at one of the 7 hubs or online. We are incredibly excited about our lineup of speakers, and hope that you submit an abstract to contribute too! More information and registration links at: meehubs.org
Final version of our last paper is out! www.nature.com/articles/s41...
Plasmids promote antimicrobial resistance through insertion sequence-mediated gene inactivation - Nature Microbiology
Inactivation of chromosomal genes through plasmid-encoded IS elements is an extended mechanism of antimicrobial resistance evolution in bacteria.
nature.com
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 👇🏼
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 6mo agoFitness effects of antimicrobial resistance genes in changing environments https://www.biorxiv.org/content/10.64898/2026.03.06.710025v1
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
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...
pnas.org
New paper out in @pnas.org, and it made the cover! 👁️ We represent plasmids as circles and mutations as dots, resembling an eye, because in this paper we literally 𝑤𝑎𝑡𝑐ℎ plasmids evolve. ‼️Check Paula’s 🧵 and the paper👇 𝗣𝗹𝗮𝘀𝗺𝗶𝗱 𝗺𝘂𝘁𝗮𝘁𝗶𝗼𝗻 𝗿𝗮𝘁𝗲𝘀 𝘀𝗰𝗮𝗹𝗲 𝘄𝗶𝘁𝗵 𝗰𝗼𝗽𝘆 𝗻𝘂𝗺𝗯𝗲𝗿 www.pnas.org/doi/10.1073/...
Paula Ramiro-Martínez@paularamiro.bsky.social · 7mo agoNew paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...
In this paper, we combined theory and experiments to study how stress can induce cooperation, and how this cooperation can promote tolerance under resource limitation. * * Stress doesn’t always break systems — sometimes it reorganizes them.
This is a very beautiful paper from the dissertation of @daniireyes.bsky.social in @ayari.bsky.social lab on how species interactions matter for antibiotic resistance.
Dani Reyes-Gonzalez@daniireyes.bsky.social · 8mo agoIn this paper, we combined theory and experiments to study how stress can induce cooperation, and how this cooperation can promote tolerance under resource limitation. * * Stress doesn’t always break systems — sometimes it reorganizes them.
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...
cell.com
Do plasmids evolve faster 🐇, slower 🐢, or just like chromosomes 🧬? In our new paper, we tackled this question using theory, simulations, bioinformatics, and experiments! 👇 Check out all the details in Paula’s thread! Hint: 🐇 (most of the time)
Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate
Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...
biorxiv.org
Paula Ramiro-Martínez@paularamiro.bsky.social · last yr.New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇
New paper alert! 🚨 Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate. We combine theory, simulations, experimental evolution, and bioinformatics to demonstrate that mutation rates scale with plasmid copy number. Let's dive in! 🧵👇
Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate
Plasmids are autonomously replicating DNA molecules that stably coexist with chromosomes in bacterial cells. These genetic elements drive horizontal gene transfer and play a fundamental role in bacter...
biorxiv.org
🚨🚨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...
nature.com
New preprint led by @brunoluviano.bsky.social & Fernando Santos. We show that filamentation enhances bacterial survival under toxic stress — not as collateral damage, but as a regulated morphological response. TL;DR: Filamentation isn’t a symptom, it’s a strategy! www.biorxiv.org/content/10.1...
🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...
Mobile integrons encode phage defense systems
Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...
science.org
We are recruiting! We are looking for a PhD student to study rapid adaptation to stress in bacteria (shorturl.at/sr0Mj). Come join us in Barcelona!
Institut de Biologia Evolutiva (IBE)@ibe-barcelona.bsky.social · 2y ago📣 Exciting News! The Evolutionary Microbiology Lab is hiring: 📍 The #IBE seeks a PhD Student. 📆 Application Deadline: 31st of March. #JoinTheIBE and be part of our team! ✍️https://www.ibe.upf-csic.es/work-with-us/job-offers
Check out this amazing Spotlight on our recently published paper -> www.cell.com/trends/micro... Huge thanks to @oliviakosterlitz.bsky.social, Benjamin Kerr and Elisabeth Duan for this great spolight.
Agents of change: a partnership between mobile genetic elements facilitates rapid bacterial adaptation
While the evolutionary interests of mobile genetic elements may differ from those of their bacterial hosts, these elements can be beneficial for their hosts by delivering, disrupting, or activating ge...
cell.com
Alfonso Santos Lopez@asantoslopez.bsky.social · 2y agoIf you like plasmids, insertion sequences, and bacterial evolution, you'll like this one! Now published in its fancy journal format. Thanks to everyone involved in the project, especially Jorge Sastre-Dominguez, @sanmillan.bsky.social and the fundación "la Caixa". nature.com/articles/s41...
Our paper on plasmid-driven heterogeneity is finally out! www.nature.com/articles/s41... @sanmillan.bsky.social @ayari.bsky.social @jerorb.bsky.social @craigmaclean.bsky.social
Thanks Thanks to @ayari.bsky.social for inviting me to present at @meehubs.bsky.social from the Cuernavaca hub. Got some great questions from the audience in other parts of the World!
Only a bit more than 12 hours till start of #MEEhubs2024. We have hundreds of registered participants, some shared their location and where they travel to on the map below! #MicroSky
Can we predict AMR evolution?? We sure can try! New study published today in PNAS www.pnas.org/doi/10.1073/...