Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Genome-scale CRISPRi profiling reveals metabolic vulnerabilities of uropathogenic Escherichia coli in human urine https://www.biorxiv.org/content/10.1101/2025.10.31.685768v1

Thinking only of Rosalind Franklin today, and what was stolen from her (and so many other female scientists alongside her).

🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63

Bacterial Halloween mask crafted by uniquely talented MSc student Dominic Spichtig - the team of Enea @phagemuffin.bsky.social is setting new standards in the lab! 🎃🔥🧬

Happy to see this hit the public! A story worth checking out that started back during my days as master student 🧑‍🔬🧬🦠

Day 22, GOAT. The most iconic (if not the greatest phage of all time) in terms of looks are myovirus like phages. They look like a lunar lander and are instantly recognisable as a virus. #Drawtober #SciArt #PhageSky

Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.

For those of you working on tailed #phages, this is the virus realm for you! #Duplodnaviria #virus #taxonomy The Profile in #JGenVirol provides the citable reference. More details in the chapter on the ICTV website: ictv.global/report/chapt...

Day 4, Claw. Phages don't really have claws, but they do have tail fibres that recognise receptors on host cells and clamp on, allowing phage particles to infect their hosts. #drawtober #SciArt #Phagesky

📢 OUR 2025 FELLOWSHIP CALLS ARE NOW OPEN 📢 🎓PhD Fellowship 👉 nccr-antiresist.ch/join-us/ 👩‍⚕️Research Fellowship in Infection and Treatment for clinicians 👉 nccr-antiresist.ch/join-us/ #TransformingAntimicrobialResearch #AMR @biozentrum.unibas.ch @unibas.ch

Viral AlphaFold Database (VAD) is live in Science Advances ~27,000 predicted viral protein monomers & homodimers Conserved folds across bacteria, archaea & eukaryotic viruses New toxin–antitoxin system KreTA uncovered Vast “functional darkness” remains uncharted www.science.org/doi/10.1126/...

That’s really cool. Every lab should have it!

www.nature.com/articles/s41... #microsky

Happy to share that the paper describing Autocycler is now 100% up: doi.org/10.1093/bioi... (1/3)

It is not only antibiotics but also certain viruses – known as bacteriophages – that can kill off pathogenic bacteria. However, Switzerland lacks the legal framework for the use of these viruses in therapy. What would need to change? Researcher Alexander Harms explains. ethz.ch/en/news-and-...

Had a short but sweet visit to Zürich to speak at @ethz.ch. Many thanks to @phagemuffin.bsky.social and @aharms485.bsky.social!

I can confirm this applies to postdocs too 😇😁

One technician position (80-100%) Group Médéric Diard Start date: 1 November 2025 or as per agreement @biozentrum.unibas.ch @unibas.ch s.ch www.biozentrum.unibas.ch/open-positio... #job #research #Hiwi #biology #science #basel #recruiting #career

Writing a recommendation letter for yourself

Thrilled to share our two latest papers with the @tcostalab.bsky.social lab! In the first, we uncover a new mechanism of satellite transfer: cf-PICIs hijack tails from diverse phages to spread across species. @imperialcollegeldn.bsky.social www.cell.com/cell/fulltex...

Uropathogenic #Ecoli #UPEC proliferate as round coccoid cells during intracellular infection; @alaskapokhrel.bsky.social @bill-lab.bsky.social &co show that accelerated division via FtsZ constriction drives this, the coccobacillus form persisting for generations @plosbiology.org 🧪 plos.io/4gdx97i

🚨 New preprint! 🧬 𝐏𝐡𝐚𝐠𝐞-𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 (𝐏-𝐏𝐬) are fascinating elements: both 𝐭𝐞𝐦𝐩𝐞𝐫𝐚𝐭𝐞 𝐩𝐡𝐚𝐠𝐞𝐬 and 𝐩𝐥𝐚𝐬𝐦𝐢𝐝𝐬 ➡️ tricky to detect. We present 𝐭𝐲𝐏𝐏𝐢𝐧𝐠 — the first 𝐢𝐝𝐞𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐜𝐥𝐚𝐬𝐬𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐭𝐨𝐨𝐥 🛠️designed specifically for P-Ps: ✅ Accurate ✅ Sensitive ✅ Easy to use 📖 www.biorxiv.org/content/10.1...

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...

Preprint: De-novo design of proteins that inhibit bacterial defenses Our approach allows silencing defense systems of choice. We show how this approach enables programming of “untransformable” bacteria, and how it can enhance phage therapy applications Congrats Jeremy Garb! tinyurl.com/Syttt 🧵

Good morning, Interlaken - fantastic venue for the annual meeting of the Swiss Society for Microbiology! 🇨🇭🏞️🦠

I cannot fully put into words what publishing this Review has meant to me, so I leave you with how we closed the paper. "The humble bacterium is still a relevant tool for the study of the underlying mechanisms that are conserved throughout life." 🧪🧫🧬📚 doi.org/10.1093/gene...

(1/5)For over a century, the hunt for new antibiotics has focused almost exclusively on bacteria and fungi. Today, that paradigm shifts. By coupling state-of-the-art AI with the vast, largely uncharted diversity of Archaea, we open a new frontier for molecular discovery.

🚨 Highly recommended position open as Scientific Officer at the NCCR AntiResist consortium - a unique opportunity to play a central role in this fantastic research setup! 🦠🧬💊

Are we placing bets yet on which fairly-reputable journal will be first to announce that they are incorporating AI into reviewing to modernize & keep up with increasing paper volumes (*cough*) - but *don't worry* they have a *specially designed system* and it will be *fine*?

The wonderful dynamics of (p)ppGpp, big thank you to everyone involved with this story www.nature.com/articles/s41...

🚨 New preprint 🚨 My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky www.biorxiv.org/content/10.1...

Excited 🥳 to share our latest work on gut phages! Big thanks to @epcrocha.bsky.social, Erick D, Camille d'H, @fplazaonate.bsky.social, Quentin LB, and all others involved for support and contributions! 🙌 Out in Cell Reports @cp-cellreports.bsky.social doi.org/10.1016/j.ce... Here's what we found 🤓

ICYMI: New online! Experimental evolution in an era of molecular manipulation

Phage DisCo! Our targeted phage discovery method in press today: journals.asm.org/doi/10.1128/... Perfectly timed with our four summer undergrad's first successful phage hunt... disco lights in the lab to mark the occasion 🕺

🧵 Why the obsession with p < 0.05 is hurting science. A meme. A truth. A reality check.

Do you have any “published” E. coli phage? and willing to share for academic research? most phages from yr 1980-2015 ish aren’t even available to researchers. they are either lost bcz of not sharing or archiving in registries.

Do you know who Douglas Prasher is? Many don't, even though he is the person who cloned the original #GFP gene in the late 1980s. In my short history of plant light #microscopy I also cover a bit of his story - & why he is relatively unknown today, despite the importance of his work. See this 🧵👇

Microbiology Monday: To swim or to swarm? 🦠While c-di-GMP inhibits swimming to promote biofilm formation in E. coli, elevated levels of the secondary message molecule trigger production of a surfactant (colanic acid) that aids swarming. #mBio: asm.social/2pm

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

Check out this really cool chance to win A LOT of free DNA synthesis via @rootpath.com! I was selected to be part of a review panel for this giveaway so write up a tweetable 280char project proposal and show us what you've got!

1/ 🧬 A Hitchhiker’s Guide to Long-Read Genomic Analysis is out now! This mini-review walks through the latest advances in long-read DNA sequencing — from assemblies to variant calling to epigenetics. Link 🔗 genome.cshlp.org/content/35/4... 🧵👇

"That telomere phages are so prevalent means that they are a selective force, one that we know little about. We now want to understand how the telomere-toxin is secreted and also understand how this ‘telocin’ wheedles its way into unsuspecting bacterial neighbors” www.science.org/doi/10.1126/...

Question for #phage aficionados: We have some phages that are each interesting, e.g., because they target a novel receptor or are only distantly related to any other viruses. What would be a good journal to publish small papers with a basic characterization for each of them? 🤔🧬

Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis? Thanks! Please RT. 🦠🙏

I am thrilled to share the first manuscript from the Wiles lab! We present "Phollow", an in vivo phage-tagging approach that enables direct observation of phage outbreaks with single-virion resolution by live imaging. Here some highlights 👇 www.nature.com/articles/s41...

New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!

The BASEL collection of E. coli #phages is limited by its host strain. @humollidorentina.bsky.social @damienpiel.bsky.social @aharms485.bsky.social &co use a modified host to add 36 new phages, revealing roles of O-antigen in recognition & R-M systems in immunity @plosbiology.org 🧪 plos.io/4jirGvX

And here it is, the completed BASEL collection finally published as early access in @plosbiology.org - see the thread for more details. 🤗🧬🎣