Rubén de Dios

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.

Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58 | Science Advances www.science.org/doi/10.1126/...

The critical human pathogen Acinetobacter baumannii exhibits light-regulated circadian rhythms Communications Biology - Gene expression studies in the critical pathogen Acinetobacter baumannii identified the existence of daily rhythms displaying a robust response to light, as well as...

Acinetobacter exhibits cyrcadian rhythms! These bugs can predict the light cycles and adjust the expression of genes accordingy. Amazing collaboration with Alejandra Mussi's team from Rosario, Argentina, my city!!
rdcu.be/eIQzL

Jobs View the current job vacancies at the Microbiology Society.

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Applications close 15 September: microb.io/jobs

Coming back from a great time visiting Karolinska Institutet and lovely Stockholm 🇸🇪

Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio

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

The evolutionary replacement of restriction-modification by Ssp antiviral systems is associated with the distribution of prophages in the major clonal group of Acinetobacter baumannii | mBio Acinetobacter baumannii is a bacterium of great concern in clinical contexts due to the plasticity of its genome and its resistance to antibiotics. Its cells are infected by a multitude of bacteriophages, and the bacterium defends itself with dozens of ...

Today, our UPOBioinfo group presents the defensome of Acinetobacter baumannii.
Do you know about its concerning Global Clone 2? Well, part of its success could be due to the replacement of restriction-modification systems by Ssp antiviral systems.

Want to name a real virus? I have recently discovered 9 new phages which now need names! To enter, you simply need to donate to the Cystic Fibrosis Trust on my JustGiving page (£2 = 1 entry) and share your email with me on donation (see link info). Please share 💚 www.justgiving.com/page/meaghan-c-1

Super excited to share our paper online 🚨today🚨 in Cell Host & Microbe‬! Xiaomei Ren @xiaomeiren.bsky.social and Mason Clark @rmasonclark.bsky.social‬ co-led discovery of ecological factors for Acinetobacter baumannii carriage in the gut, a reservoir for pathogen spread. 🎉

tinyurl.com/443kfefk

The combination of active partitioning and toxin-antitoxin systems is most advantageous for low-copy plasmid fitness - Nature Communications Effe et al. evaluate how specific plasmid traits influence plasmid fitness; they provide mechanistic insight into the persistence of large conjugative plasmids, including those that disseminate antibi...

Happy to finally share this! Read here about the best strategy the the persistence of low-copy plasmids. @mariosanter.bsky.social @iwangtoknow.bsky.social doi.org/10.1038/s414...

On our way to Niagara Falls for the Acinetobacter Conference 2025 after a fantastic stay-over in lovely Toronto with @lharkova.bsky.social. We will miss the pancakes with maple syrup 🥞

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...

Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins systems provide bacteria with an adaptive immune system against exogenous sequences, such as pla...

New paper published in our computational biology group for the study of phages, of which we are especially proud: "Bacteriophages in Pseudomonas aeruginosa evade the CRISPR-Cas I-F system by depletion of PAM sequences".

It’s been fantastic to talk about my adventures with Acinetobacter plasmids at the @mgeworkshop.bsky.social. Such a lovely meeting with lots of great science and cool people. See you next year!

Congrats Marta!

Host range and ARG dissemination are shaped by distinct survival strategies of conjugative plasmids Horizontal gene transfer is a major driver of bacterial evolution and the global dissemination of antibiotic resistance genes (ARGs). Conjugative plasmids play a crucial role in ARG spread across host...

🎉 So proud of our PhD student, Ryuichi ONO, who submitted his first first-author paper from his undergrad research @utokyoofficial.bsky.social about plasmid survival tactics influencing ARG spread! Now just wait to see what he’s been cooking up in our lab 🤩

www.biorxiv.org/content/10.1...

Glad to contribute to @uk.theconversation.com explaining our latest paper on plastic-eating pathogens 🦠
In case you missed it: www.cell.com/cell-reports...

Plasmid–bacteria associations in the clinical context Antimicrobial resistance (AMR) is one of the most pressing global health problems, with plasmids playing a central role in its evolution and dissemination. Over the past decades, many studies have inv...

New opinion paper from the lab!

www.cell.com/trends/micro...

🔎 From antibiotic resistance to boredom research, the #YERUNResearchMobilityAward helped two early-career researchers take big steps forward. Meet Ruben de Dios Barranco & Muireann O'Dea in the latest YRMA Voices👇
yerun.eu/2025/05/yrma...

Mobile integrons encode phage defense systems Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

🧪
Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉

Short 🧵
www.science.org/doi/10.1126/...

My first adventure with P. aeruginosa finally saw the light! It was really fun to work on this exciting project and definitely worth the effort!

MGE Workshop

We are pleased to announce that registration for 3rd MGE Workshop is now live!

If you are interested in giving a talk please register online through our website by Friday 16th May.

We look forward to seeing you all in Southampton in June!

www.ukmgeworkshop.org

A palette of bright and photostable monomeric fluorescent proteins for bacterial time-lapse imaging Bright and photostable monomeric fluorescent proteins enable long-term time-lapse imaging in E. coli.

Our set of new prokaryote-optimized fluorescent proteins is now published ! #microbiology #microsky #microscopy 🧫🦠🔬
www.science.org/doi/10.1126/...

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China - Nature Communications The genomic epidemiology of Acinetobacter baumannii, which is rising in virulence and multidrug resistance, was explored. This study examined bloodstream infection isolates from Chinese patients in 20...

Interesting paper

Genomic epidemiology and phylodynamics of Acinetobacter baumannii bloodstream isolates in China

'A. baumannii is evolving from a low-virulence, multidrug-resistant pathogen to a more virulent one'

www.nature.com/articles/s41...

George Church, el genio rebelde que sueña con crear un parque temático de especies ‘resucitadas’ El padre de la biología sintética aspira a revivir un mamut con las herramientas de edición genética, un proyecto con claroscuros, como el resto de su brillante carrera

Este artículo de @aberron.bsky.social en @eldiario.es con un perfil del investigador irrepetible que es George Church, dinamizador de la genética moderna, iconoclasta, responsable de experimentos que otros tildan de imposibles y visionario, merece una lectura atenta.
www.eldiario.es/sociedad/geo...

The evolution of antibiotic resistance in Europe, 1998–2019 Author summary Antibiotic resistance is an important public health threat: resistant infections are currently associated with 5 million deaths per year globally. This burden may increase further in th...

New paper: long-term trends in antibiotic resistance show signs of stabilisation (thread). journals.plos.org/plospathogen...

Pseudomonas syringae subpopulations cooperate by coordinating flagellar and type III secretion spatiotemporal dynamics to facilitate plant infection Nature Microbiology - Single-cell gene expression analysis reveals phenotypic heterogeneity to enable bacterial specialization over the course of plant colonization.

How Bacteria Outsmart Plants—Then Flee the Scene!

#MicroSky #PlantScience #Pseudomonas

Our new research in Nature Microbiology uncovers the sophisticated teamwork of Pseudomonas syringae, a notorious plant pathogen.

🔗 rdcu.be/egczU

3rd UK MGE Workshop – June 16-17, Southampton

Low-cost, science-focused, and full of fresh faces! Tea, biscuits, dinner, and… karaoke!

Call for talks– No abstract needed! Just send your title by the end of April.

Spread the word!

#MGE #UKscience

Bye bye Liverpool! It’s been a lovely #Microbio25 Conference! So much awesome research presented and so many awesome people gathered!