Structural basis for DNA processing and membrane translocation by ComEC in natural transformation Natural transformation is one of the major pathways of horizontal gene transfer in bacteria, enabling the acquisition of extracellular DNA and its integration into the host genome. ComEC is a membrane...

ComEC structure is out!! 😍
Congratulations to the authors! That’s not an easy one. We have been trying for years to get that structure…
We failed and gave up.

Pictures from Fanny Martinez Real and Stefan Mundlos🙏

This year, the annual symposium of my Chaire @college-de-france.fr will be on The Evolution of Developmental Mechanisms. An impressive lineup of speakers and weirds animals, including humans. Free entrance and coffee breaks. Come, have a seat, relax and enjoy the best possible basic science🤘RT🙏

Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

🔈Paper out! We turned the most fascinating phage host-switch mechanism, diversity-generating retroelements, into a programmable mutagenesis tool, DGRec. You can perform targeted hypermutation of any 50-200bp sequence directly in vivo in E. coli www.nature.com/articles/s41...

Finally published. Many thanks to a wonderful collaborative team and scientific platforms!!! And thanks to editors and reviewers for enthusiasm and a great review.

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

Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design The role of genome 3D organization for fundamental chromatin processes, such as long-range promoter-activator regulatory interactions, remains ambiguo…

Happy to share our review of the past, recent, and future applications of synthetic genomics in studying the 3D functional organization of chromosomes, a set of approaches that are gaining momentum!

www.sciencedirect.com/science/arti...

Fast and accurate multiple-protein-sequence alignment at scale with FAMSA2 - Nature Biotechnology FAMSA2 accurately aligns millions of protein sequences at high speed.

10 years after the first FAMSA paper, its successor is now published in Nat Biotech! We believe that FAMSA2 can enable analyses of large protein collections that were previously unattainable. Thank you, Andrzej and Cedric, for great collaboration
www.nature.com/articles/s41...

Postdoctoral position in mosquito population genomics at Institut Pasteur in Paris - Research The Insect-Virus Interactions Unit is looking for a postdoctoral researcher to investigate the genomic variations underlying a mosquito’s capacity to transmit human arboviruses. Description Our resear...

🚨 A #postdoc position is available @lambrechtslab.bsky.social @pasteur.fr ➡️ Come join our team to investigate the #genomic variations underlying the adaptive potential and vectorial capacity of Aedes aegypti #mosquitoes 🦟 More details at this link: research.pasteur.fr/b/1Cov

We (with @dornhaus.bsky.social) finally wrote up our class on how to teach modeling to biologists, which ends up being a non-trivial exercise in understanding the roles that theory plays in the scientific method. We hope others will use our class, or simply enjoy the manuscript!

Evolution of pandemic cholera at its global source - Nature The seventh cholera pandemic, driven by El Tor Vibrio cholerae, evolved separately in Bangladesh and India, with the Ganges Basin acting as the global source, and its evolution has been shaped by...

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

#phage #phagesky #microsky

Excited to share our new paper out today in @science.org 🎉

We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩

Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...

Multiple fully funded PhD/postdoc positions available: experimental evolution of tumour suppression, egalitarian & fraternal ETIs, jumbo phage ecology & genetics. Related EoIs welcome.

Email CV/statement of motivation written in own words. Open until filled.

Grateful for reposting 🙏

Just a few days left to apply to one of these postdoc positions in my Unit at @pasteur.fr!

Join our department (GEE) as a fellow - Research Career Development Fellowships Program Call: tinyurl.com/2sfpyhsz

GEE invites #ECRs who wish to be sponsored to apply for external fellowships to establish an independent research group. @ucllifesciences.bsky.social

More info: tinyurl.com/mtwhwzjj

📣 Two weeks left to apply! 📣
I2BC is recruiting new team leaders in molecular and cellular biology, with special attention to multidisciplinary approaches and computational biology. 🧬🧪🔬👩‍🔬🧑‍💻
We provide a great environment with top-notch technological facilities.

🗓️ Apply by April 22, 2026!

Actually, what is a gain-of-function mutation? Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien

academic.oup.com/genetics/adv...

Also thanks to Lyndall & @psarkies.bsky.social, @ahocher.bsky.social, and members of the lab for their comments and Francis Barr @oxfordbiochemistry.bsky.social for encouraging me to write down my thoughts. 2/2

Finally, oysters serve as hotspots of horizontal gene transfer betw bacteria, mediated by mobile genetic elements. Which, considering the high density of bacteria in marine animals (rel. environment), could be quite general. Great work led by Jeff Liang, Karine Cahier. With @fredoleroux.bsky.social

Second, one can indeed identify the same virulent phage years later with few or no changes in an open marine environment. Hence, coevolving phage-bacteria populations can exhibit complex dynamics, with rapid replacement of some lineages alongside multi-year persistence of others.

Our ms on re-sampling 4 years apart vibrio phage in natural environments is now out with some improvements. First, clearer evidence of cryptic population dynamics between phage and vibrio, presumably because of genetic diversity. www.nature.com/articles/s41...

Forecasting Multitrait Resistance Evolution under Antibiotic Stress Abstract. Many bacteria rely on efflux pumps to survive antibiotic stress and exposure to antibiotics often leads to mutations in pump genes or their regul

@suvamroy.bsky.social @elibbyscience.bsky.social & @peteralind.bsky.social modeled gene expression in P. aeruginosa efflux systems, analysing how the complex regulatory networks associated with efflux pumps might evolve under antibiotic treatments.

🔗 doi.org/10.1093/molbev/msag065

#evobio #molbio

Want to annotate a bacterial genome with structures?

@oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures

www.biorxiv.org/content/10.6...

#phagesky #microsky #microbiomesky

Latest from the lab!
Between clinical S. aureus, most gene transfer mechanisms are blocked, yet lateral transduction remains highly efficient.
Restriction modification-defective strains act as gateways for horizontal gene transfer, enabling DNA flow across populations. rdcu.be/fbNQK

Our perspective on measuring individual virus traits, led by staff scientist @antanij.bsky.social
#phagesky #microsky

Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here

📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.

How diverse is bacterial immunity ?

We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...

Explore them here defensefinder.mdmlab.fr/wiki/refseq_...

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Phages communicate across species to shape microbial ecosystems Gallego-del-Sol et al. show that arbitrium-coding phages can sense non-cognate peptide signals from other phages to regulate lysis-lysogeny decisions. This crosstalk affects lysis-lysogeny outcomes of...

This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up.
Grateful (and slightly humbled) to be part of this. Thanks Alberto!
www.cell.com/cell/fulltex...

Open Positions -

Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications.
Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101

Rapid resistance evolution against phage cocktails Abstract. When bacteria are treated with multiple antibiotics simultaneously, resistance is highly unlikely to evolve. In contrast, resistance against mult

Rapid resistance evolution against phage cocktails

#ISMEJournal by Baltus van der Steen, Matti Gralka, and @yuvalmulla.bsky.social

academic.oup.com/ismej/advanc...

What happens when Klebsiella's capsule locus is swapped? Unexpectedly little in terms of cell growth. Yet, it does change the bacterium's environment and interactions with it: evolution by seamless plug-and-play capsule swap. Led by @julielebris.bsky.social @olayarendueles.bsky.social