Rubén de Dios

In our most recent work David Forrest has discovered a widespread mechanisms linking transcription initiation to DNA supercoiling...

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

#MicroSky: Plasmid vectors still underpin molecular biology, but convenience shouldn’t trump design. De Lorenzo & Martínez revisit copy number, selection & stability, and explores modular AI-assisted vector design for robust synthetic biology across the microbial world. doi.org/10.1111/1751...

Is AI hurting your ability to think? How to reclaim your brain AI is replacing tasks we have grown reluctant to do ourselves – thinking, writing, creating, analysing.

AI is replacing tasks we have grown reluctant to do ourselves – thinking, writing, creating, analysing.

Emerging advances in prokaryotic transposition: TnPedia as a promising tool TnPedia provides a curated framework for understanding prokaryotic transposable elements (TEs), including general and historical information and basic concepts, while integrating mechanistic insights, family-level classification, and representative examples. It summarizes key developments reshaping the field, including RNA-guided transposition, and provides information on TE acquisition and transmission of antimicrobial resistance-associated transposons.

Emerging advances in prokaryotic transposition: TnPedia as a promising tool

Phenylacetic acid mediates Acinetobacter baumannii entry into a viable but non-culturable state Desiccation tolerance is central to the pathogenic success of the opportunistic pathogen Acinetobacter baumannii, allowing its survival on hospital surfaces in the absence of water and nutrients for m...

Delighted to share our latest work exploring the regulation of desiccation tolerance in Acinetobacter baumannii. Great effort by @lharkova.bsky.social and @rdedios.bsky.social

www.microbiologyresearch.org/content/jour...

Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.

SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria

journals.asm.org/doi/10.1128/...

Coupling DNA processing to early gene expression drives antibiotic resistance plasmid dissemination https://www.biorxiv.org/content/10.64898/2026.01.09.698686v1

Starting 2026 with a hike to the castle on top of my hometown Jaén. Lovely views to kick off the year.

Diagram of genes required for in vivo fitness in different organs displayed as bar graphs

Gene dependence during mammalian Acinetobacter baumannii pneumonia and septicaemia infections. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen... #MGen #PublishAndRead

Selective elimination of donor bacteria enables global profiling of plasmid gene expression at early stages of conjugation Abstract. Conjugative plasmids are a major driving force for the dissemination of antimicrobial resistance. During conjugation, plasmid DNA is transferred

academic.oup.com/nar/article/... Collaboration with Y. Yamaichi. Killing donor bacteria in conjugation mixes using water enables transcriptomic profiling of early plasmid genes ! Superb tool for studying zygotic induction of these early genes, which include anti-SOS and anti-RM factors. #microsky

Research institutes: What makes the magic? Beyond the great science, what makes a research institute special? Do the work environment and the organisational structure support researchers in delivering their best outputs? Does the culture help ...

Research institutes: What makes the magic?

Was fun to help my old boss Sarah Teichmann and her friend Frank Bradke put this piece out for the FEBS Network. A reflective follow-up to our PLOS Biology article in 2023. With art by the amazing Catherine Bone

network.febs.org/posts/resear...

comic of a happy person with a shitty 1st draft

I just got an email from a former mentee telling me that one dinner conversation changed how he writes papers♥️

I told him: “just write the paper, get it out—the next one will be better, and the next even better.”

Perfectionism is a trap (and a way to procrastinate...:))

An updated evolutionary classification of CRISPR–Cas systems including rare variants - Nature Microbiology An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

After 5 years of waiting, the new #CRISPR classification by Makarova et al. is out @natmicrobiol.nature.com www.nature.com/articles/s41...

Paul Nurse describing the main job of a PI

(From ‘The Thinking Game’, 2024)

Thanks Patri!

New adventures, same old fantastic companions. @lharkova.bsky.social and I just joined @sotonbiosciences.bsky.social at @unisouthampton.bsky.social with the whole @ronanmccarthy.bsky.social lab. Looking forward to collaborating with such a great research community!

“What Grant Reviewers Actually Look For (and What They Ignore)” A close colleague of mine at a major US research university begins the process of preparing a grant proposal by creating something he calls a “storyboard”.  When I was growing up in LA, the concept…

"What Grant Reviewers Actually Look For (and What They Ignore)" jim-olds.org/2025/10/23/w...

Thrilled to share our multidisiplinary work on how genome-wide DNA bridging by H-NS reshapes the stationary phase bacterial nucleoid and affects the transcriptional landscape. With Xindan Wang and @meyerroc.bsky.social
www.biorxiv.org/content/10.1...

q.e.d Science Critical Thinking AI for constructive criticism and science evaluation

Here's the link to the system, try it! qedscience.com
@qedscience.bsky.social

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.

We're hiring! We are looking for a Publishing Operations Editor to join our friendly team! You’ll support the strategic growth of our journal portfolio by managing the peer review process and overseeing production services.

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