Paula Ramiro-Martínez

New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story www.pnas.org/doi/10.1073/...

Last week at #ISPB2026 ✨🥨 Another #ISPB full of exciting science! Such a great time with amazing people, finally meeting some, catching up with friends, and getting really cool feedback on this new project 🐘 Already looking forward to Toronto!

Finally out! 🎉 After 3 years of postdoc in London, here is my main work, now published in Nature Comm. (and as co-corresponding author!) Using a combination of bioinformatic and experimental approaches, we propose a model of plasmid evolution in Staphylococcus. www.nature.com/articles/s41... ⬇️ 1/4

It’s out! 🥹🎉 We’re so incredibly happy and proud to see this work out in the world. And once again, a huge thank you to the great mastermind @jaescudero.bsky.social and all the co-authors; this wouldn’t have been possible without you! doi.org/10.1038/s415... @natmicrobiol.nature.com

Big news! Deeply honored to receive an #ERCStG from @erc.europa.eu! 🍾 Over the next five years, E-MOTION will study how interactions between Mobile Genetic Elements shape bacterial evolution in clinical settings. Exciting science and opportunities ahead: stay tuned, positions will be opening soon!

Bacterial Mercury Resistance Reveals a Robust Species-Structured Human Antimicrobial Mobilome https://www.biorxiv.org/content/10.64898/2026.06.26.734528v1

New paper out! 🔈 Genomic Characterization of the RyC collection: 50 Multidrug Resistant Clinical Isolates of Escherichia coli and Klebsiella spp. 50 MDR gut isolates, 2 sequencing platforms, 4 “omes,” and 1 mission: provide a resource to decode AMR and MGE dynamics www.biorxiv.org/content/10.6...

🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇

What if multireplicon plasmids are not an oddity, but an evolutionary strategy? We found that they are common, more mobile, broader-host-range, and enriched in AMR. Even more interesting: their assembly doesn’t look random. 👀 Paper preprint: www.biorxiv.org/content/10.6... Thread below!🧵👇

What happens when Klebsiella's capsule locus is swapped? Unexpectedly little in terms of cell growth. Yet, it does change the bacterium's environment and interactions with it: evolution by seamless plug-and-play capsule swap. Led by @julielebris.bsky.social @olayarendueles.bsky.social

We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

Final version of our last paper is out! www.nature.com/articles/s41...

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 👇🏼

➡️ 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? 🤔 🧵👇

Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5

New preprint out on bioRxiv! www.biorxiv.org/content/10.6... Can conjugative plasmids be used to control plasmid and pathogen spread? Follow me down the rabbit hole that led to this story 🧵

What a fantastic new addition to my lab! 🚀 Welcome @albertohca.bsky.social to the @uam.es family! Stay tuned for the science we’re going to build together in the coming years!

A short research stay in 2019 (back in the pre-COVID era) at José R. Penadés lab turned into the third chapter of my PhD and today it finally sees the light.

🧬New paper out! We report the first isolation of viable B. bacteriovorus predators from human gut microbiota. www.frontiersin.org/journals/mic.... Great work of Mario Romero @migueldiezfdz.bsky.social @josete600.bsky.social and @rosacampo.bsky.social

In this issue: Fresh light on horse evolution, mangrove restoration as coastal flood protection, and the links between aerobic metabolism and planetary oxygenation. In PNAS: https://ow.ly/yB6J50Y5ykK

And what a beautiful @pnas.org cover @paularamiro.bsky.social and @jerorb.bsky.social !!!!!! You should be very proud!

So great to finally have such a clear answer to this question!! Well done guys!

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/...

We're thrilled that, in addition, our figure has been chosen as the cover for this issue of PNAS! 🥹🎉

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

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...

#NewResearch The long-term existence of diverse virulent phages within cultures of Escherichia coli and others challenges the virulent–temperate dichotomy and points to non-canonical phage lifestyles. #MicroSky 🦠 @peterdoug.bsky.social @emggroupucph.bsky.social www.nature.com/articles/s41...

#NewResearch Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle. #MicroSky 🦠 www.nature.com/articles/s41...

🎁 Getting a paper acceptance right before Christmas break is one of the best feelings. 100% recommend. Happy holidays, everyone! 🎄✨

A pleasure and an honour to have received this prestigious grant with my admired colleagues and friends @sanmillan.bsky.social and @asanchezlab.bsky.social . More about AMR under plasmid lens!. My sincere gratitude to @caixaresearch.bsky.social @microryc.bsky.social @esgem-sg.bsky.social

A plasmid golden ratio? 🧬 Plasmid copy number ≈ 2.5% of chromosome size—consistent across bacterial species! pmc.ncbi.nlm.nih.gov/articles/PMC... @jerorb.bsky.social 🧪 #microbesky

In episode 337 TWiM explains a study that examines pathogen presence in ancient humans and concludes that zoonoses emerged 6500 years ago with the domestication of livestock, and determination of universal rules that govern plasmid copy number. This week's special guest: @markowenmartin.bsky.social

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

Our new manuscript is out! A bit of everything cool: Plasmids ✅ Insertion Sequences ✅ AMR Evolution ✅ Microbial Communities ✅ Databases analyses ✅ Mathematical modeling ✅ See the scientific thread below of Jorge Sastre, who has brilliantly led this work with @palomarodera.bsky.social

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...

🚨🚨 New paper in @narjournal.bsky.social! 🍾 Excludons are pairs of overlapping genes that block each other’s expression (basically, reverse operons). We built a tool to identify them in bacterial genomes using transcriptomic data, in an awesome collab led by Iñigo Lasa and Álvaro San Martín. 👇

Had an amazing time at #FEMS2025 last week, where I presented our latest findings on collateral sensitivity mediated by beta-lactamases ☯️ Big thanks to everyone who came by! So proud of my colleagues for their brilliant talks and posters ✨

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)

The must-read of this Summer! 🤩 Congrats to all the authors for this beautiful work 🥳