Paula Ramiro-Martínez

➡️ 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 🧵

Equipazo!!

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.

Frontiers | Genome assembly and functional predation analysis of novel Bdellovibrio isolates from human gut microbiota IntroductionPredatory bacteria of the Bdellovibrio and like organisms (BALOs) have long been postulated as living antimicrobials, yet their occurrence and ec...

🧬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

Pictured is a map of plasmids, which are DNA molecules that can be transferred between bacteria. Each ring and dot represents an evolved plasmid and a mutation, respectively. Image credit: Paula Ramiro-Martínez.

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!

Muchas gracias Teresa!! 🫂

Thank you Álvaro!!!

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

Thank you so much!!!

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! 🥹🎉

Huge thanks to all my brilliant co-authors 🙌

@nachodequinto.bsky.social, @laura-jaraba.bsky.social , Val F. Lanza, @crisherencias.bsky.social, Adrián González Casanova, @penamiller.bsky.social & @jerorb.bsky.social

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 🫧🤩

What about natural plasmids?

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

💥 Result: 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 higher PCN, the boost in mutation supply outweighs the segregational drift 💥

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

We evolved bacterial lines for 30 days under tight bottlenecks at three conditions:
🔹low (~1)
🔹medium (~10)
🔹high (~60 copies)

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: Mutation rate increases with PCN, but with diminishing returns: a logarithmic rise.

Plasmids face a paradox.

🔹 More copies = more mutational opportunities 📈
🔹 But random segregation = more drift, fewer fixations 📉

So, which force dominates as plasmid copy number (PCN) increases: more mutations or more losses?

Let’s find out 🧬

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/...

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...

Persistent virulent phages exist across bacterial isolates - Nature Microbiology 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.

#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...

Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.

#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...

Early Xmas present 🎅🏼

🎁 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