Paula Ramiro-Martínez
@paularamiro.bsky.social
📤 172
📥 129
📝 35
Predoctoral researcher at evodynamics lab in Madrid. Bacterial and plasmid evolution 🫧🧬💻
pinned post!
New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story
www.pnas.org/doi/10.1073/...
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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...
https://www.pnas.org/doi/10.1073/pnas.2526088123
about 2 months ago
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Eduardo Rocha
6 days ago
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
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From Trading Genes to Crafting New Tricks: How Horizontal Gene Transfer Potentiates the Emergence of Novel Functions
https://ecoevorxiv.org/repository/view/12209/
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Alvaro San Millan
10 days ago
Final version of our last paper is out!
www.nature.com/articles/s41...
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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.
https://www.nature.com/articles/s41564-026-02290-x
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Alberto HCA
13 days ago
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 👇🏼
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Jorge Moura de Sousa
21 days ago
➡️ 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? 🤔 🧵👇
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https://www.biorxiv.org/content/10.64898/2026.02.27.708500v1
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Eduardo Rocha
19 days ago
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
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Pedro Dorado-Morales
25 days ago
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 🧵
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https://www.biorxiv.org/content/10.64898/2026.02.25.707879v1
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Alfonso Santos Lopez
about 1 month ago
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!
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Pedro Dorado-Morales
about 1 month ago
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.
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Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Targeted elimination of Staphylococcus aureus mastitis infections with synthetic phage-based CRISPR-Cas delivery systems
https://www.nature.com/articles/s41522-026-00931-x
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Cristina Herencias
about 2 months ago
🧬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
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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...
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2026.1752098/full
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Proceedings of the National Academy of Sciences
about 2 months ago
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
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Teresa M. Coque
about 2 months ago
And what a beautiful
@pnas.org
cover
@paularamiro.bsky.social
and
@jerorb.bsky.social
!!!!!! You should be very proud!
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Alvaro San Millan
about 2 months ago
So great to finally have such a clear answer to this question!! Well done guys!
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Jerónimo Rodríguez-Beltrán
about 2 months ago
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/...
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We're thrilled that, in addition, our figure has been chosen as the cover for this issue of PNAS! 🥹🎉
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about 2 months ago
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New paper out in PNAS!!! 🎉 Do more plasmid copies mean faster evolution? 🧵 Dive into the story
www.pnas.org/doi/10.1073/...
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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...
https://www.pnas.org/doi/10.1073/pnas.2526088123
about 2 months ago
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Paula Ramiro-Martínez
Eduardo Rocha
2 months ago
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🧵
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Manuel Ares-Arroyo
2 months ago
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...
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https://www.biorxiv.org/content/10.64898/2026.01.13.699239v1
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Nature Microbiology
3 months ago
#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...
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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.
https://www.nature.com/articles/s41564-025-02207-0?utm_source=bluesky&utm_medium=social&utm_campaign=nmicrobiol
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Nature Microbiology
3 months ago
#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...
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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.
https://www.nature.com/articles/s41564-025-02203-4?utm_source=bluesky&utm_medium=social&utm_campaign=nmicrobiol
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Jerónimo Rodríguez-Beltrán
3 months ago
🎁 Getting a paper acceptance right before Christmas break is one of the best feelings. 100% recommend. Happy holidays, everyone! 🎄✨
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Teresa M. Coque
4 months ago
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
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AnniZLab: [🦠, 🧬 , ✨]
6 months ago
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
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Microbetv
7 months ago
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
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TWiM 337: Lifestyles of the plasmids
YouTube video by MicrobeTV
https://youtu.be/GrWwvWb9yJ0?feature=shared
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Alicia Calvo-Villamañán
7 months ago
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
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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...
https://rdcu.be/eBhe3
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Alfonso Santos Lopez
7 months ago
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
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Jorge Sastre Domínguez
7 months ago
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...
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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...
https://www.biorxiv.org/content/10.1101/2025.08.12.669853v1
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Jerónimo Rodríguez-Beltrán
8 months ago
🚨🚨 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. 👇
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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
https://academic.oup.com/nar/article/53/14/gkaf686/8211924
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Laura Álvaro-Llorente
8 months ago
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
8 months ago
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
8 months ago
The must-read of this Summer! 🤩 Congrats to all the authors for this beautiful work 🥳
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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! 🧵👇
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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...
https://www.biorxiv.org/content/10.1101/2025.07.21.665944v1.article-metrics
8 months ago
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bioRxiv Microbiology
8 months ago
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 🦦
8 months ago
This is a legitimately incredible result that hints at something fundamental about plasmids that we don’t yet understand
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Jerónimo Rodríguez-Beltrán
8 months ago
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
9 months ago
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...
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naturepoker
9 months ago
Oh this is fantastic 🦠🧫
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Javier DelaFuente
9 months ago
If you're into plasmid biology, you can't miss this back-to-back by two inspiring teams!
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Jerónimo Rodríguez-Beltrán
9 months ago
🚨🚨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...
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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...
https://www.nature.com/articles/s41467-025-61202-5
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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 👇
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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...
https://doi.org/10.1038/s41467-025-61202-5
9 months ago
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Paula Ramiro-Martínez
Ana Elena Pérez-Cobas
11 months ago
New mini-review on the respiratory microbiome and its contribution to human health from biotechnology 🫁🦠
@tmcoque.bsky.social
@microbiotech.bsky.social
enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
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The Respiratory Tract Microbiome and Human Health
The respiratory tract microbiome (RTM) trains the immune system and protects against infections. Changes in the RTM are linked to various respiratory diseases. High-throughput methodologies and compu...
https://enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.70147
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Alicia Calvo-Villamañán
about 1 year ago
Happy International Day of Women and Girls in Science 👩🔬🧬
#womeninscience
#girlsinscience
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Ignacio (Nacho) de Quinto
about 1 year ago
Just migrated here from twitter! Hello everyone. Also, I've just put up a super simple (and free) to use APP to streamline experiment design and result analysis of 96 (or 384) wells plate experiments for my lab pals. You can try it here:
rosettier.streamlit.app
Feedback is very welcome 😁!
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Rosettier
A free, user-friendly web application for planning 96 or 384-well plate experiments. Rosettier si...
https://rosettier.streamlit.app
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Jerónimo Rodríguez-Beltrán
about 1 year ago
Really beautiful day receiving the “Margarita Salas” Award from the Madrid Region! Really proud to share it with my colleagues, friends and family!!
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