Competition against the intestinal microbiota selects for pathoadaptive traits in ESBL E. coli https://www.biorxiv.org/content/10.64898/2026.06.25.730905v1

We are recruiting a lab manager for my group in Oxford. This is a lovely team doing great things, and you could be an important part of it! See here: www.path.ox.ac.uk/vacancy/lab-... Please spread the word!

Lab Manager - Molecular Immunology - Dunn School

Laboratory Manager/Senior Scientist position in the Molecular Mucosal Immunology group at Oxford

path.ox.ac.uk

🔥 Published today, and just in time for summer conferences, here are your guidelines for presenting badly www.nature.com/articles/s41... rdcu.be/fqa92

Phage hunting never gets boring 😁

Alexander Harms@aharms485.bsky.social · 2mo ago

New phages from school workshops are coming to the lab! Yasmina Stolber in our group works with Enea @phagemuffin.bsky.social to phenotype and sequence them - but it's crazy how much the phenotyping and experience already allow us to deduce their taxonomic classification 🧫🧬😎.

The "Research Day" at our department D-HEST is always caleidoscope of exciting science from food over health to medicine. Phage biotechnology was well represented with Dorentina @humollidorentina.bsky.social and Enea @phagemuffin.bsky.social from our group and the lab of Martin Loessner. 🧫🧬🍻

Writing a manuscript is like making a documentary. Instead of a film, it’s in writing and figures. Writing a proposal is like writing evidence based science fiction.

🎊 New Preprint from phagefoundry.org ! Super excited to share our latest work on generating systematic phage-MDR P. aeruginosa interaction dataset & use of ML to predict phage susceptibility & phage cocktails from target genome sequences alone, w validations www.biorxiv.org/cgi/content/...

Some phages are named after gods or rivers, this one was named by journalist Thilo Mischke @thilomischke.bsky.social after his grandma ("Oma Karin") while filming in our lab. It's a cool phage that should be temperate but became virulent due to a transposon at its lysogeny control! ⛓️‍💥💪🏼

📢 Registration for our International Symposium on “New Concepts in Prokaryotic Virus-Host Interactions” is now open! 🗓️ 5–7 October 2026 📍 Harnack House, Berlin, Germany ➡️ Information and registration: spp2330.de/symposium-20...

Small fun story from the lab about a slightly crazy rabbit hole or "guess what's living in your agar?" - all the details in the thread by Enea @phagemuffin.bsky.social 👇🏼🔥

Enea Maffei@phagemuffin.bsky.social · 3mo ago

1/6 👻 Something strange in your liquid agar? Who you gonna call? Thermophile hunters. Our new @asm.org #MRA paper reports the complete genome sequence of Geobacillus stearothermophilus strain CS7089 isolated from a commercial agar preparation.

1/6 👻 Something strange in your liquid agar? Who you gonna call? Thermophile hunters. Our new @asm.org #MRA paper reports the complete genome sequence of Geobacillus stearothermophilus strain CS7089 isolated from a commercial agar preparation.

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

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

📣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.

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

Did you know? 🧵 1/3

Fantastic snow excursion of the lab together with our friends in Martin Loessner's group 🏔😁☀️

🚨Preprint! Happy to share the research from my PhD “Genome delivery of a contractile tailed phage and its superinfection exclusion mechanism”. We use cryoEM to study the genome ejection of the phage T4, revealing how the tape measure protein regulates the process. www.biorxiv.org/content/10.6...

Ooooh. Cool new paper on origins of life. A simple 45-nucleotide RNA molecule that can perfectly copy itself. www.science.org/doi/10.1126/...

A small polymerase ribozyme that can synthesize itself and its complementary strand

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

science.org

Excited to share first preprint from our lab! @giubotti.bsky.social found that antibiotic tolerance in multispecies biofilms follows a surprising spatial pattern: cells survive only at intermediate distances from a partner species. 🦠 Preprint: doi.org/10.64898/202...

It seems that NCBI GenBank is currently not active beyond the repository itself and has also been unresponsive to requests for a while already. Do you think this may be a transient inconvenience or a sign that we should explore alternatives such as ENA at EMBL-EBI?

What could mirror bacteria do in nature if created? A story of these prospects and a plan to prevent them. Titles aside, I hope you'll read it (the tech is NOT close). Thanks to Tom Freeman for writing help & @jfischman.bsky.social for ace editing! www.scientificamerican.com/article/life...

Life’s evil twins, called mirror cells, could wipe us out if scientists don’t stop them

Researchers are close to making “reversed” cells that may wipe us off the planet

scientificamerican.com

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Protein structure-informed bacteriophage genome annotation with Phold

Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.

academic.oup.com

George Bouras@gbouras13.bsky.social · 12mo ago

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

We've got ISSUES. Literally. We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do? arxiv.org/abs/2601.07563 A 🧵 1/n

As the year ends, we decided to select our favorite papers of 2025 Turns out, it is impossible as we love them all! So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology. Here is a glimpse into #EditorPicks of 2025 #MicroSky 🦠

Do you relate to this as well?

During the Cold War, US President Reagan put nuclear war in clear words: “A nuclear war cannot be won and must never be fought. The only value in our two nations possessing nuclear weapons is to make sure they will never be used. But then would it not be better to do away with them entirely?”

ICYMI, this new preprint is just awesome. "Here, we show that O-antigen–dependent trade-offs between pathogenicity and interbacterial competition have persisted for over two centuries in natural P. viridiflava populations." www.biorxiv.org/content/10.1...

Persistent trade-offs balance competition and colonization across centuries

Microbial competition drives rapid adaptation, often forcing organisms to specialize in new ecological niches. Adaptations that improve competitive ability can reduce performance in other environments...

biorxiv.org

Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY

KlebPhaCol paper is now out! Go check it out and see all that we offer. And when ready, visit our website for more: www.klebphacol.org

KlebPhaCol

klebphacol.org

Nucleic Acids Research@narjournal.bsky.social · 9mo ago

⭐ NAR Breakthrough! ⭐ A community-driven collection uniting 52 phages, 74 Klebsiella isolates, and extensive genomic + phenotypic data — all freely available at klebphacol.org. 🧬 Learn more: doi.org/10.1093/nar/... @fnobrega.bsky.social @danielarothschild.bsky.social #antimicrobialresistance

Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science. The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7

An archaeal genetic code with all TAG codons as pyrrolysine

Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...

scim.ag