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Jerónimo Rodríguez-Beltrán

@jerorb.bsky.social

920 followers 570 following 65 posts

We study Antibiotic Resistance Ecology and Evolution · Ramón y Cajal University Hospital · Madrid · www.evodynamicslab.com

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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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DaganLab @daganlab.bsky.social · 10h

Happy to introduce SegMantX. Analyzing #plasmid we find that most duplications are MGE-driven. Additional use cases include detection of DNA transfer between replicons and examination of plasmid sequence similarity. Try it out! doi.org/10.1093/molb...

SegMantX: a novel tool for detecting DNA duplications uncovers prevalent duplications in plasmids

Abstract. Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification an

doi.org

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Michael Brockhurst @brockhurstlab.bsky.social · 2d

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...

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...

www.biorxiv.org

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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 2d

And the crispri genetic interaction screen 👏💫🤯 #microsky from J-W Veening lab. Dual CRISPRi-seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle: Cell Systems www.cell.com/cell-systems...

Dual CRISPRi-seq for genome-wide genetic interaction studies identifies key genes involved in the pneumococcal cell cycle

Dénéréaz et al. introduce dual CRISPRi-seq, a broadly applicable method to chart gene-gene interactions across whole genomes. Applying it to the pathogen Streptococcus pneumoniae, they uncovered over ...

www.cell.com

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Craig MacLean @craigmaclean.bsky.social · 9d

New pre-print: Eco-evolutionary responses of phage to different thermal regimes.

Great work led by Sam Greenrod and fun collaboration with Kayla King's lab.
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www.biorxiv.org/content/10.1...

Evolutionary rescue accelerates competitive exclusion in a parasite community

Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

www.biorxiv.org

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Craig MacLean @craigmaclean.bsky.social · 8d

New pre-print
Competition between phage constrains adaptation to thermal fluctuating temperatures.
More work led by Sam Greenrod in collaboration with @kayla-king.bsky.social lab.
#Phagesky#Microsky

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

www.biorxiv.org

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Tami Lieberman @contaminatedsci.bsky.social · 9d

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

www.biorxiv.org

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Michael Brockhurst @brockhurstlab.bsky.social · 12d

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

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

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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · 12d

Synthetic lethal TN-seq! #microsky 🦠

Sarah Svensson @campy-bara.bsky.social · 12d

Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...

Dual transposon sequencing profiles the genetic interaction landscape in bacteria

Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...

www.science.org

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Zamin Iqbal @zaminiqbal.bsky.social · 12d

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

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Craig MacLean @craigmaclean.bsky.social · 13d

New ERC funded computational postdoc position in my lab! We are looking for someone who will study the genomics of bacterial evolution using samples from experimental evolution and clinical trials. Lots of opportunities for interesting and fun collaboration!
my.corehr.com/pls/uoxrecru...

Job Details

my.corehr.com

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Michael Brockhurst @brockhurstlab.bsky.social · 13d

Recent paper from the lab studying predictors of phage cocktail efficacy against complex clinical Pseudomonas populations

royalsocietypublishing.org/doi/epdf/10....

Led by Rosanna Wright with extraordinary MSc (PhD) student Maisie Czernuska

Bacteria–phage infection network structure and genomic defence system content predict efficacy of a phage therapy cocktail against Pseudomonas aeruginosa from chronic lung infections

royalsocietypublishing.org

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 15d

Divergent spontaneous antibiotic-resistance evolution confers reciprocal and exploitable collateral sensitivity effects https://www.biorxiv.org/content/10.1101/2025.09.22.677096v1

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Agathe couturier @agathe-couturier.bsky.social · 21d

Exclusion systems, far from slowing down plasmid spread, are in fact essential to preserve host cell viability and thereby ensure the successful dissemination of conjugative plasmids and antibiotic resistance genes.

@nfrk92.bsky.social
@narjournal.bsky.social

academic.oup.com/nar/article/...

Exclusion systems preserve host cell homeostasis and fitness, ensuring successful dissemination of conjugative plasmids and associated resistance genes

Abstract. Plasmid conjugation is a major driver of antibiotic resistance dissemination in bacteria. In addition to genes required for transfer and maintena

academic.oup.com

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Eduardo Rocha @epcrocha.bsky.social · Sep 8

Willing to join us @pasteur.fr for a PhD for a project on how interactions between mobile genetic elements shape bacterial adaptation? Subject to be tailored to candidates with keen interest in evolution, genomics, computational biology, microbiology. Check www.pasteur.fr/en/education...

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Tami Lieberman @contaminatedsci.bsky.social · 26d

We are looking for a postdoc to study single-cell transcriptional heterogeneity in the human skin microbiome.

We have a new protocol mostly developed, but need someone to see it through. Experience with protocol dev or RNAseq appreciated.

Funded by a new grant from MIT-HEALS.

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Reposted by Jerónimo Rodríguez-Beltrán

Zamin Iqbal @zaminiqbal.bsky.social · 28d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Zeynep Baharoglu @zeynepbaharoglu.bsky.social · Sep 6

So excited our antibiotic potentiation story is out 🤩 Led by the extraordinary @manonlang.bsky.social with @fox-science.bsky.social & @amazeld.bsky.social +amazing collaborators @immunobladder.bsky.social @imaneelmeouche.bsky.social 🦠 We believe it can make a difference in #AMR infections!

Uridine as a potentiator of aminoglycosides through activation of carbohydrate transporters

Uridine boosts aminoglycoside treatment efficiency against antibiotic-susceptible as well as antibiotic-resistant E. coli strains.

www.science.org

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DaganLab @daganlab.bsky.social · Sep 5

A call for W 3 (full) professorship in Molecular and Evolutionary Zoology is now open at our department. Join our community of evolutionary biologists! Excellent facilities and scientific environment!
www.nature.com/naturecareer...

W 3 professorship in Molecular and Evolutionary Zoology - Kiel, Schleswig-Holstein (DE) job with Christian-Albrechts-Universität zu Kiel | 12844416

Kiel University aims to attract more qualified women to professorship positions. The Institute of Zoology at the Faculty of Mathematics and Natural...

www.nature.com

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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Sep 2

PanGene-O-Meter: Intra-Species Diversity Based on Gene-Content https://www.biorxiv.org/content/10.1101/2025.09.01.673544v1

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Michael Baym @baym.lol · Sep 1

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics

Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...

www.microbiologyresearch.org

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bioRxiv Genomics @biorxiv-genomic.bsky.social · Sep 1

Efficient detection and typing of phage-plasmids https://www.biorxiv.org/content/10.1101/2025.08.29.673033v1

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James McInerney @jomcinerney.bsky.social · Aug 29

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes

Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

www.biorxiv.org

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Antimicrobial resistance #AMR @antimicrobial.bsky.social · Aug 30

UCLA Health ended an NDM-1 Pseudomonas aeruginosa outbreak by tracing it to an ICU sink biofilm via whole-genome sequencing, then eliminating it with targeted disinfection, plumbing changes, and staff education—showcasing the power of diverse IPC measures.

#AMR

www.newswise.com/articles/the...

These Techniques Stopped the Outbreak of an Antibiotic-Resistant Bacteria in a SoCal Hospital | Newswise

Researchers detected Pseudomonas aeruginosa, a common hospital-acquired bacterium, often found in moist environments. But this strain carried a gene called New Delhi metallo-β-lactamase (NDM-1), an en...

www.newswise.com

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Eduardo Rocha @epcrocha.bsky.social · Aug 27

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

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Timothy Fuqua 🏳‍🌈 @timothyfuqua.bsky.social · Aug 28

Excited / nervous to share the “magnum opus” of my postdoc in Andreas Wagner’s lab!

"De-novo promoters emerge more readily from random DNA than from genomic DNA"

This project is the accumulation of 4 years of work, and lays the foundation for my future group. In short, we… (1/4)

De-novo promoters emerge more readily from random DNA than from genomic DNA

Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

www.biorxiv.org

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