This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

New online! Revisiting the life cycle of temperate phages

🔬🦠 Comment #Klebsiella parvient-elle à changer de capsule aussi fréquemment pour mieux s’adapter à son environnement ? Les travaux de @julielebris.bsky.social mis à la une par @cnrsbiologie.bsky.social 👏 -avec @epcrocha.bsky.social #MicroSky @cbitoulouse.bsky.social

Our paper examining the evolution of halophily in DPANN is out now in MBE! academic.oup.com/mbe/advance-...

Revised story Systematic receptor mapping in acapsular Klebsiella www.biorxiv.org/content/10.6...

Glad that our paper is out today in @cp-cellhostmicrobe.bsky.social A baby received a routine course of amoxicillin. In that infant's #gut 💩, we could see something remarkable, already present **before** the antibiotic arriveda single strain 🦠 of #Akkermansia muciniphila was already running 1/n

Please share widely! Abstract submissions open for the 2026 Jacques Monod conference: Ecology and evolution of host-parasite interactions in a changing world! Held in beautiful Roscoff France from November 2- 6, 2026. Abstracts submission deadline : June 6 cjm.sb-roscoff.fr/en/conferenc...

#ResultatScientifique🔎| Une bactérie capable de changer de « bouclier » pour mieux s’adapter à son environnement : une stratégie étonnante de Klebsiella pneumoniae qui éclaire ses capacités d’évolution et de résistance. ✍️ @olayarendueles.bsky.social @julielebris.bsky.social ▶️ buff.ly/q8AKHo1

Registration opened for our International Symposium of SPP 2330! This is going to be phage-tastic meeting in Berlin! Highlight of the second funding period! @spp2330.bsky.social, @dfg.de

I had fun writing a short commentary on the importance of integrating prophage biology into microbiome research 🦠 Now out in @cp-cellhostmicrobe.bsky.social #microbiomesky #phagesky www.cell.com/cell-host-mi...

New paper out in @molbioevol.bsky.social 🧬🦠 We show phage toxin diversity in protective symbionts isn’t random—toxin families are linked to defense against different parasitoid species. This suggests toxin diversification is a major force shaping the functional evolution of these microbes.

More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

I’ve started my SNSF Ambizione Group Leader position at the University of Zurich 🧬 We will study plasmid evolution, plasmid interactions, and CRISPR-Cas systems to better understand antibiotic resistance spread. Very grateful to everyone who supported me along the way.

🚨 New preprint from the lab! 🚨 We show that multireplicon plasmids are true AMR "jack-of-all-trades": Widespread, highly mobile, broad host-range, and packed with resistance genes. Far from random, they form co-evolving associations driven & 𝘮𝘢𝘪𝘯𝘵𝘢𝘪𝘯𝘦𝘥 by IS elements. See Nacho's thread below!👇👇

👋 Transposon lovers: registration is now open for the CSHL TE meeting! We have a 🔥 lineup of invited speakers and many slots for short talks selected upon abstract across all areas of TE biology. 🧬➰🧬 #TEsky Abstract deadline: July 10 meetings.cshl.edu/meetings.asp...

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

The Metappuccino paper is out in Bioinformatics! academic.oup.com/bioinformati... Given an input list of SRA sample IDs, Metappuccino infers and normalizes metadata over 15 categories, specially aimed at human transcriptomics studies 1/3

Polish phage science meets Polish visual storytelling 🇵🇱🦠 To celebrate our last paper, we collaborated with an artist who previously worked on The Witcher 3 — to create a comic about phages and why understanding them matters in the fight against antibiotic-resistant bacteria. Comic below 👇

This one means a lot. Our paper, “Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome,” is out! doi.org/10.1038/s414...

Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...

Berruga-Fernández et al. show that bacterial hybrid chromosome formation driven by conjugative mobile genetic elements may be an important and widespread mechanism in the emergence and evolution of high-risk bacterial pathogens. 🔗 doi.org/10.1093/molbev/msag085 #evobio #molbio #bacteria

Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...

🎉 New in @plosbiology.org: Temperate phages of Klebsiella pneumoniae show capsule-driven host tropism — but how? The working assumption was depolymerases: enzymes that chew through the bacterial sugar capsule. Turns out that's not the whole story. 🧵 journals.plos.org/plosbiology/...

We have a PhD studentship available to develop genome safeguarding technologies for synthetic phage therapeutics www.findaphd.com/phds/project... It is part of an exciting new @officialuom.bsky.social PhD by Enterprise programme www.bmh.manchester.ac.uk/study/resear...

📜The final version of our paper on eCIS firing is out: www.nature.com/articles/s41... Congrats to @xujwet.bsky.social @chipericson.bsky.social #cryoEM #CIS

Today Is the deadline for abstract submissions ‼️

Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.

A new family of rolling-circle replication endonucleases widespread in archaeal viruses and plasmids. This family is unrelated to the HUH superfamily Reps, but distantly related to the bacterial Rep_trans enzymes. @narjournal.bsky.social academic.oup.com/nar/article/...

@xavierdidelot.bsky.social et al. present the R package DiagnoDating for diagnosing issues in a reconstructed dated phylogeny, including outlier detection, posterior predictive checking, and residual analysis. 🔗 doi.org/10.1093/molbev/msag093 #evobio #molbio #compbio #phylogeny

New online! Phage host range: determinants, dynamics and applications

We are hiring a PhD candidate! Only for non-EU graduates. To work on the molecular and genomic epidemiology of Treponema pallidum, based on our recent publication (doi:10.1128/mbio.00358-26). Interested? Send your CV and an expression of interest to [email protected] before May 20th, 2026.

Integrating theory and machine learning to reveal determinants of plasmid copy number www.nature.com/articles/s41...

"The selfish ribosome" paper is now published in @plosbiology.org . Have a look! Many thanks to the editors and reviewers! doi.org/10.1371/jour...

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.

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🙏

🔈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...

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...

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...

🚨 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!

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!

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

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...