🚨 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

The JEDI marker - a new approach for measuring #biodiversity that captures all domains of life and is applicable across biological and ecological scales. It's time to change the way we perceive biodiversity - www.biorxiv.org/content/10.1...

Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...

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...

Come and be my colleague at the Dunn School! It‘s a brilliant place to work and exciting to be building up our immunology team. Do apply. Do pass on the news 💉🧬🦠🔬🧫

🎉 We’re excited to share our very first preprint!! 🎉 "Metabolic Crossroads: AMDHD2 Couples the Hexosamine Biosynthetic Pathway to Acetyl-CoA Homeostasis in Pluripotent Stem Cells" 👉 doi.org/10.1101/2025... #FirstPreprint #StemCells #Metabolism #Epigenetics #AcetylCoA #HBP #Pluripotency #NewScience

How diverse are E. coli capsules? How are they linked to ecology and disease? Find out with > 25,000 genomes and MAGs including undersampled environments and hosts from all over the world. Great genomics - glycobiology synergy in Sunagawa and Slack groups at ETH! www.biorxiv.org/content/10.1... 🧪🧫🔬

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

As a first-year oncology fellow at Memorial Sloan Kettering in New York City I had the privilege of rotating through all of the clinics. Lung, beast, ovarian, leukemia, lymphoma. 1/7

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

Looking forward to #EESMicrobiology and excited to present our latest work on E. coli capsules on Friday! www.embl.org/about/info/c...

Check out this framework for de novo protein design by @mjendrusch.bsky.social and Kashif Sadiq! Happy we could contribute with our favourite phage defence system.

Habemus pubScan! 🎉 Introducing pubScan, a new way to explore your PubMed publications through the lens of co-authorship. 🔍 Check it out at: pubscan.expressrna.org ❤️ Love it? Show your support by liking, sharing, and spreading the word. #pubscan

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution. New paper from the lab, and the third chapter of Lars Zandbergen’s thesis! www.biorxiv.org/cgi/content/...

Our paper has been selected among Editors' Highlights for Microbiology! @natcomms.nature.com www.nature.com/collections/... 🧪🔬🧫

Here are our ideas on developing tools and technologies for anaerobic bacteria! We hope you enjoy the read as much as we enjoyed brainstorming on the topic...

Do we really know the antibiotics that we already have? Check out our story on 60y old drug nitroxoline and its new tricks! @goetheuni.bsky.social @embl.org www.nature.com/articles/s41... + great piece from the synchrotron @esrf.fr where we chased nx effects on metals www.esrf.fr/home/news/ge...

New study by @mucosalimmunology.bsky.social (Dunn School and @ethzurich.bsky.social) with Médéric Diard (@biozentrum.unibas.ch) reveals how combining vaccines with friendly bacteria can boost vaccination efficacy and potentially reduce reliance on antibiotics www.path.ox.ac.uk/news-article...

I am very excited to share our latest publication on the effect of systemic #endotoxin on intestinal #microbiota spearheaded by the brilliant Sanne Kroon at the Hardt lab @eth-dbiol.bsky.social @ethzurich.bsky.social @naturecomms.bsky.social 👉🏼 rdcu.be/eelLn

Excited to share our paper published in @currentbiology.bsky.social that explores the consequences of having multiple genomes in a bacterial model system and it’s benefits in a multidrug environment ! www.cell.com/current-biol...

Brochado and Maier labs in Germany are looking for a PhD student to study horizontal gene transfer in bacteria. ENDAMR Marie Curie doctoral network (endamr.eu) - an amazing opportunity to work with top scientists in the field all around Europe! www.cmfi.uni-tuebingen.de/mariecuriephd

Interested in microbial #metabolism, #mucosalbiology and #UTI? Then check out the open postdoctoral position in the Mucosal Immunology Group at ETH Zurich! NB: All applications must go via the ETH job portal: www.jobs.ethz.ch/job/view/JOP... Closing date: 24th Feburary 🧪🧫🔬

"The world has been through anti-science cycles before" not microbiology related, but a 🧵 worth reading

You want to learn about microbiology from a fantastic lineup of speakers on a beautiful Greek island? PhD students apply now for the @EMBO | @FEBSnews Lecture Course The New Microbiology! Registration: 1 Apr 2025 Course: 03 – 11 Sep 2025 | Spetses, Greece meetings.embo.org/event/25-new...

More than 60 German-speaking universities and research institutes have just jointly announced they will cease activities on X because “the current orientation of the platform is not compatible with their core values” incl. scientific integrity, transparency and democratic discourse” 🧪

What is the diversity of antiphage systems out there ? We used protein and genomic language models (and defense score!) to start bringing some answers: >45 000 protein families. Leb by E. Mordret. www.biorxiv.org/content/10.1... Interactive UMAP to have fun mdmparis.github.io/antiphage-la...

Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...

Delighted that @tarnopol.bsky.social’s paper (dissertation ch.) is online @currentbiology.bsky.social! “Experimental horizontal transfer of phage-derived genes to Drosophila confers innate immunity to parasitoids.” Phage toxin genes became a feature of insect immune systems millions of years ago…👇🏼

Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55

Interested in antibiotic cross-resistance/sensitivity? Tired of experimental evolution? Then check our new story led by brilliant @nazgulsakenova.bsky.social, now out on Nature Microbiology @naturemicrobiol.bsky.social !

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

Thoughts on O-Antigen Variation by Roberto — The O-side chains of lipopolysaccharides (LPS), the outer most feature of most Gram-negative's outer membrane, are highly variable in terms of their chain length and chemical composition. In my last post... Read more > tinyurl.com/54fzpdd9 #MicroSky

Trying to fit “high-throughput bacterial viability assay” in the acronym TETRIS

Honed by many rounds of collaborative paper writing with PhD students and postdocs, my list of 24 scientific writing tips: www.huber.embl.de/group/posts/... Subjective and personal, but hopefully useful for somebody.

New collaborative work from our lab on the transmission of AMR in a community context. www.biorxiv.org/content/10.1... We find that Gram positive bacteria, particularly enterocci, increase the conjugation efficiency of uropathogenic E.coli.

Please add microbiome-related conferences for 2024 in this thread. Thanks.

I’ll be in Stockholm (Karolinska) for a seminar and for talking all things mucosal-immunology-related next week! news.ki.se/calendar/int... Zoom options also available I think. I’m looking forward to some exciting exchanges!

🦠 Do microbiomes have their own microbiomes? 🦠 Well... kind of. Much smaller than bacteria, there is a whole zoo of Darwinian entities that depend on microbial hosts. We could call these collectives "nanobiomes", and there's much to explore! 🧵 A thread (originally on Twitter, now on Bsky) ⬇️

Not enough people know about bioicons.com Open source vector graphics. Free alternatives to BioRender.

We have published a manuscript describing a software tool to reduce ambiguity and improve interpretability in microbial GWAS, called panfeed. Here's a quick explainer: www.microbial-pangenomes-lab.org/2023/11/09/M... And here's the link to the paper: www.microbiologyresearch.org/content/jour...