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Reposted by Paula Ramiro-Martínez

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 29d

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

a Scatter plots showing the correlation between plasmid size (x-axis) and PCN (y-axis) for the analysed genera. Each point represents the median PCN and plasmid size for each PTU, and error bars indicate the standard deviation from the median. Grey lines represent ordinary least squares regression, with the surrounding shaded area indicating 95% confidence intervals. The scaling factor or slope, k, is indicated on each panel. b Distribution of total DNA load per plasmid (x-axis) relative to chromosome size per genus (y-axis). The DNA load of each plasmid is calculated by multiplying the plasmid size by the copy number and then expressed as a proportion relative to the chromosome size. The point inside the box marks the median. The upper and lower hinges correspond to the 25th and 75th percentiles, and whiskers extend to 1.5 times the interquartile range. Only Escherichia and Salmonella significantly differ from All; Kruskal–Wallis test followed by Dunn’s test for pairwise multiple comparisons p < 10−4; effect size = 0.006. c Relative plasmid DNA load observed (%) (x-axis) and expected (y-axis) per cell. The y-axis indicates the expected plasmid DNA load (%) inside a cell when it contains one plasmid (1n), two plasmids (2n), and so on. This expected data has been calculated by generating a sequence from 1 to 9 multiplied by the median of the DNA load per plasmid (2.49%). Each green point represents a single genome, and the black points are the median for each category. Shading indicates interquartile ranges. Pearson’s p value and coefficient are shown for the correlation between expected and observed plasmid DNA.

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Microbetv @microbetv.bsky.social · Aug 19

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

TWiM 337: Lifestyles of the plasmids

YouTube video by MicrobeTV

youtu.be

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Alicia Calvo-Villamañán @aliciapcv.bsky.social · Aug 20

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

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...

rdcu.be

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Alfonso Santos Lopez @asantoslopez.bsky.social · Aug 13

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

Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

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...

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...

www.biorxiv.org

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Jorge Sastre Domínguez @jorgesastred.bsky.social · Aug 13

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...

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...

www.biorxiv.org

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 29

Thanks!!!!

Reposted by Paula Ramiro-Martínez

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 25

🚨🚨 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.

👇

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

academic.oup.com

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Laura Álvaro-Llorente @lauralvllo.bsky.social · Jul 23

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 ✨

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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 22

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)

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Ana Elena Pérez-Cobas @anaelenaperezcobas.bsky.social · Jul 22

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

Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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...

www.biorxiv.org

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

Thirty days of evolution… totally worth it! 🥹

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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! 🥳

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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 🫧🤩

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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!

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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

At more copies, mutation supply dominates drift! 💥

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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.

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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.

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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?

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 22

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...

www.biorxiv.org

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Reposted by Paula Ramiro-Martínez

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Jul 22

Plasmids promote bacterial evolution through a copy number-driven increase in mutation rate https://www.biorxiv.org/content/10.1101/2025.07.21.665944v1

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Dave Baltrus 🦦 @surtlab.bsky.social · Jul 20

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

Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 2

🚨🚨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...

www.nature.com

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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 17

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

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Jerónimo Rodríguez-Beltrán @jerorb.bsky.social · Jul 3

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...

Felipe VI, king of Spain, greeting my grandma

A selfie of some of the Prize Recipients

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naturepoker @binomicalabs.org · Jul 2

Oh this is fantastic 🦠🧫

Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 2

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨

doi.org/10.1038/s414...

We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

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...

doi.org

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Paula Ramiro-Martínez @paularamiro.bsky.social · Jul 3

Thanks Alberto!!!