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Reposted by Eduardo Rocha

Adrian Cazares @cazares-adr.bsky.social · 4d

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics

We just did that to study the history of #AMR spread @science.org
doi.org/10.1126/scie...

If you like time travel & biology, this 🧵is for you👇

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

doi.org

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Reposted by Eduardo Rocha

Paul Rainey @paulbrainey.bsky.social · 4d

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...

Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology

The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

www.evolbio.mpg.de

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Reposted by Eduardo Rocha

James McInerney @jomcinerney.bsky.social · 15d

OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4

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Gang Yu @gangyuplant.bsky.social · 5d

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

Chromosome architecture affects virulence and competitiveness in Agrobacterium tumefaciens C58

Chromosome architecture influences Agrobacterium fitness, competitiveness, and virulence, shaping its adaptation and evolution.

www.science.org

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Reposted by Eduardo Rocha

Willem van Schaik @wvschaik.bsky.social · 10d

Interesting paper

'Evolutionary selection of trimethoprim-resistant dfrA genes in lytic phages affects phage and host fitness during infection'

www.science.org/doi/10.1126/...

Evolutionary selection of trimethoprim-resistant dfrA genes in lytic phages affects phage and host fitness during infection

Lytic phages for phage therapy carry abundant ARGs that rarely spread to bacteria but enhance phage and host fitness.

www.science.org

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Reposted by Eduardo Rocha

Di Jiang @dijiang319.bsky.social · 13d

This week @science.org 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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Reposted by Eduardo Rocha

Zamin Iqbal @zaminiqbal.bsky.social · 14d

Apologies, forgot to add the actual paper link!!!!!

www.science.org/doi/10.1126/...

Pre- and postantibiotic epoch: The historical spread of antimicrobial resistance

Plasmids are now the primary vectors of antimicrobial resistance, but our understanding of how human industrialisation of antibiotics influenced their evolution is limited by a paucity of data predati...

www.science.org

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Reposted by Eduardo Rocha

Zamin Iqbal @zaminiqbal.bsky.social · 14d

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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Reposted by Eduardo Rocha

Craig MacLean @craigmaclean.bsky.social · 14d

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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Reposted by Eduardo Rocha

Alice Ledda, PhD @alicele.bsky.social · 19d

Google reminds me that it's been 2 years since this picture and the Workshop on plasmids as vehicles of AMR spread.

We did our best to reorganize it this year but we couldn't get any funding .

We haven't given up on the workshop and at some point we will organize another edition!

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Reposted by Eduardo Rocha

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19d

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Reposted by Eduardo Rocha

adameyrewalker.bsky.social @adameyrewalker.bsky.social · 18d

My first Bluesky post - it's been a time coming, but I have decided to only review for journals that are associated with academic societies. I will also focus my publication efforts in those journals as well. Our APCs should go back into the subject.

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Eduardo Rocha @epcrocha.bsky.social · 18d

Congratulations !!

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Reposted by Eduardo Rocha

Martial Marbouty @mmarbout.bsky.social · 21d

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

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

Phages with a broad host range are common across ecosystems - Nature Microbiology

Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

www.nature.com

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Reposted by Eduardo Rocha

Sophie Abby @soabby.bsky.social · 22d

Really glad to announce a new preprint from our lab: Global distribution of quinones in Bacteria! We here combine comparative genomics and text mining to leverage information on quinones distribution from thousands of articles describing new species and from dozens of thousands of genomes! 1/5

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

Global distribution of isoprenoid quinones across Bacteria https://www.biorxiv.org/content/10.1101/2025.09.17.676790v1

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Reposted by Eduardo Rocha

Agathe couturier @agathe-couturier.bsky.social · 23d

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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Reposted by Eduardo Rocha

Felix M Key @keyfm.bsky.social · 25d

Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de.

Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions.

www.mpiib-berlin.mpg.de/2193291/job_...

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Reposted by Eduardo Rocha

Alice Maestri @alicemaestri.bsky.social · 27d

We're looking for a technician at Institut Pasteur for experimental work on satellite-phage-bacteria interactions, working directly with @jmouradesousa.bsky.social and myself in the lab of @epcrocha.bsky.social ! ANR funded.

Link to the job emploi.pasteur.fr/offre-de-emp...
Thx for sharing!

INSTITUT PASTEUR - Technicien de recherche Microbiologie H/F

emploi.pasteur.fr

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Reposted by Eduardo Rocha

Institut Pasteur Education @pasteuredu.bsky.social · 27d

🚀 Applications for the PPU International PhD Program are open until October 20, 2025!

We invite you to discover 2 projects on Structural Biology & 3 Research & Technology projects 👇

📍 Program starts: October 2026

Discover all the projects & apply now: www.pasteur.fr/en/education...

Call for candidates PPU - highlight of a project

Call for candidates PPU - highlight of 2 projects

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Reposted by Eduardo Rocha

Milan Gerovac @gerovac.bsky.social · 29d

No Genetics? Try ASOs – A non-genetic approach to silence genes at the phage-host interface. We use it to study jumbo phage biology and anti-phage defence.
@jorg-vogel-lab.bsky.social @helmholtz-hiri.bsky.social
@uni-wuerzburg.de @helmholtzhzi.bsky.social
published now in @nature.com

Programmable antisense oligomers for phage functional genomics - Nature

Establishing antisense oligomers as versatile, non-genetic tools to silence phage mRNAs opens applications in basic research and biotechnology, as shown by identifying essential factors for propagatio...

www.nature.com

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Eduardo Rocha @epcrocha.bsky.social · 29d

How do loci for bacterial capsules (Klebsiella) manage to get swapped around despite their outstanding phenotypes? They just plug and play, having little impact on the rest of the genome. Kudos to @julielebris.bsky.social , check her thread below

Julie Le Bris @julielebris.bsky.social · Sep 10

How complex functions, with important physiological and evolutionary impacts get repeatedly and efficiently transferred across genomes?
That’s what we explored using one of the fastest-evolving loci in Bacteria: the capsule locus.
The paper: www.biorxiv.org/content/10.1...
Thread👇

Serotype swapping in Klebsiella spp. by plug-and-play

Understanding how complex, multi-gene systems evolve and function across genetic backgrounds is a central question in molecular evolution. While such systems often impose costs through epistatic inter...

www.biorxiv.org

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Reposted by Eduardo Rocha

Zamin Iqbal @zaminiqbal.bsky.social · Sep 10

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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Reposted by Eduardo Rocha

Deepa Agashe @deepaagashe.bsky.social · 29d

About 10 years ago, we set up lots of experimental beetle populations, censused monthly. Expecting extinction, I said the workload would drop soon. But they all rescued themselves! 😱 So Vrinda & co kept counting. Many hundreds of thousands of beetles later, we have some neat outcomes. Enjoy!

Vrinda Ravi Kumar @vrindarvkm.bsky.social · 29d

Our work on evolutionary rescue is finally out in this week's issue of PNAS! Check out the NCBS communications team piece on our work quoted below.

National Centre for Biological Sciences, Bengaluru @ncbsbangalore.bsky.social · 29d

#LatestPublication
Vrinda & team from Dr Deepa Agashe's lab tracked beetle populations for 5+ years in harsh environments. Findings show how traits of founders influenced the long-term survival of their descendants.

🔗 bit.ly/42hsviC

@deepaagashe.bsky.social

🧵Check out the thread to know more!👇

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Reposted by Eduardo Rocha

José R Penadés @jrpenades.bsky.social · Sep 9

Our second paper with @tcostalab.bsky.social and GoogleDeepMind
reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology.
www.cell.com/cell/fulltex...

AI mirrors experimental science to uncover a mechanism of gene transfer crucial to bacterial evolution

By solving a previously unsolved biological question, the AI co-scientist predicted a complex mechanism of gene transfer and generated hypotheses that opened new research directions, illustrating AI's...

www.cell.com

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Reposted by Eduardo Rocha

Schulenburg Lab Kiel @schulenburglab.bsky.social · Sep 8

We are welcoming applications for a full professorship on Molecular and Evolutionary Zoology at Kiel Univerdity, Northern Germany, with fantastic facilities and infrastructure! @uni-kiel.de @crc1182.bsky.social @transevo.bsky.social 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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