Paula Ramiro-Martínez

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

YouTube video by MicrobeTV TWiM 337: Lifestyles of the plasmids

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

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...

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

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...

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...

Thanks!!!!

ExcludonFinder: mapping transcriptional overlaps between neighboring genes Abstract. Bacteria regulate neighboring genes via overlapping transcription in untranslated regions (UTRs), forming excludons. This overlap leads to transc

🚨🚨 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 🥳

Thirty days of evolution… totally worth it! 🥹

Huge thanks to all the authors behind this paper 🙌

@nachodequinto.bsky.social, Laura Jaraba-Soto, Val F.Lanza, @crisherencias.bsky.social, Adrián González Casanova, @penamiller.bsky.social, and @jerorb.bsky.social

So excited to see it finally out! 🥳

In summary, plasmids are not just gene delivery platforms.

They significantly boost the availability of mutations, enabling rapid evolution of traits like resistance, metabolism, and virulence, highlighting their role as evolutionary powerhouses of bacterial cells.

PCN is key to evolvability 🫧🤩

Do natural plasmids show the same results?

We analyzed 1,598 plasmids (NCBI) 💻 to detect mutations arising during culture growth by comparing sequencing reads to consensus assemblies.

High-copy plasmids exhibited significantly higher mutation rates, just like theory (and experiments!) predicted!

Experiments confirm it: plasmid mutation rate rises logarithmically with copy number 🚀

At more copies, mutation supply dominates drift! 💥

We conducted a mutation accumulation experiment to test our predictions using a plasmid with a tunable copy number 🫧

We established three PCN conditions: low (~1), medium (~10), and high (~60 copies). Lines were evolved for 30 days under severe bottlenecks.

We modelled plasmid inheritance using a Cannings model and validated it with computational simulations 🧫 Each plasmid copy is like an evolutionary unit, randomly split at division, then copied.

Prediction: the mutation rate rises with PCN, but with diminishing returns, increasing logarithmically.

Plasmids face opposing evolutionary forces:

🔹 More copies = more chances to mutate 📈
🔹 But random segregation = drift, purging mutations 📉

So mutation supply ↑ with PCN, but the probability of fixation ↓

Which force dominates: the boost in mutation rate or the loss from segregational drift?

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...

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 https://www.biorxiv.org/content/10.1101/2025.07.21.665944v1

This is a legitimately incredible result that hints at something fundamental about plasmids that we don’t yet understand

People from the lab killing it

At the Duomo with friends

Super proud of the lab for their outstanding presentations at #FEMS2025 in Milano!

Science is better when you work with such a stellar team!🚀✨

@femsmicro.org

Felipe VI, king of Spain, greeting my grandma

Felipe VI and Jero

A selfie of some of the Prize Recipients

It was an honor and a joy to receive the National Research Prize for Young (!) Researchers. The highlight? My grandma greeting the King of Spain.

What a day!

www.youtube.com/watch?v=oSQP...

Oh this is fantastic 🦠🧫

Thanks Alberto!!!

If you're into plasmid biology, you can't miss this back-to-back by two inspiring teams!

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...

🚨🚨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...

Huge thanks to this amazing team for all the hard work: @nachodequinto.bsky.social, João, Val and @jerorb.bsky.social 🫧 💪

Finally, our analysis revealed that each plasmid independently accounts for a similar DNA content (~2.5% of the chromosome size) regardless of their host genus, size, or copy number. 7/7

We discovered a universal scaling law linking copy number and plasmid size, which can be used to predict the PCN of your favorite plasmid! 6/7