Welcome, @stephlo.bsky.social, our new Team Leader for Protein Function. Find out how Stephanie’s experience in genomics shaped her approach to protein curation and AI integration. #ProteinScience #AI www.embl.org/news/people-...

Some more thoughts on why this outbreak (large, happening quickly, in one place) might be happening: johnlees.me/posts/menb-o... Perhaps strain + immunity + high transmission

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

@oldenoughtosay.com I see that your house has recently been visited by the Bad Enterovirus Fairy, aka Hand, foot and mouth disease. I got so het up about baby germs that I wrote a 9.5k word review article on them (800 word version here theconversation.com/if-you-think...). Normal response, right?!

You can now view a tree of 2,399,238 bacterial genomes we made from AllTheBacteria (on the great Taxonium): taxonium.org/atb That's a big tree! (unless you're used to SC2 trees)

I always speak politely to AI as there is a non-zero chance that this will be a situation in the future:

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

The genomic diversity and spatial patterns of Mycobacterium bovis in Ireland revealed by whole genome sequencing rdcu.be/e50zT

Terrible headline (this is NOT what the new research - link below - shows!), terrible AI image! Argh! Here’s the actual research: www.science.org/doi/10.1126/... Where do I start?! 1/4

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...

Delighted to see over 17 million new protein structure predictions from novel proteins in AllTheBacteria are now integrated into the AlphaFold Database at @ebi.embl.org ! Huge work from @gbouras13.bsky.social @oschwengers.bsky.social and friends to generate these. www.ebi.ac.uk/about/news/u...

Incredible time at #AIR2026 covering breadth of respiratory infection, microbiomes and immunology with some really beautiful biology. Thanks to fellow committee members @resp-micro.bsky.social @drclairesmith.bsky.social @ewanharrison.bsky.social , Alex Kayongo and organisers @eventswcs.bsky.social

Fantastic final day at #AIR2026. A masterclass in in vitro modelling by Scott Randall followed by a great panel discussion with funders @asthmaandlung.org.uk @wellcometrust.bsky.social @cysticfibrosis.org.uk @karlstaples.bsky.social

Another insightful day of science, discussion and making new friends at #AIR2026 Day 2 Highlights: making sense of big data, spatial transcriptomics and in vitro modelling of respiratory infections @eventswcs.bsky.social @sangerinstitute.bsky.social

Always good to be back at Wellcome Genome Campus, this time for the #AIR2026 conference on Genomic and systems approaches to respiratory infection, microbiomes and immunity

How do bacterial pangenomes evolve, what controls their dynamics, why do they exist? Fitting a mechanistic model to 450 species from allthebacteria.org suggesting fast vs slow gene exchange (i.e. amount of MGEs) is a major differentiating factor, correlated with phylogeny rather than lifestyle

Startling that this is being broadcast in the absence of any public communications by @ukri.org The academic community has a right to expect to be told first hand what is happening with response mode funding and what the immediate future looks like www.researchprofessionalnews.com/rr-news-uk-r...

We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond. We extend our deepest condolences to his family, friends, and colleagues. www.embl.org/news/people-...

🫁 AIR 2026 registration closing 19th Jan Focused on respiratory infection, microbiomes and immunity, with amazing speakers. Incl genomics, single-cell, spatial and systems approaches. 📍 Wellcome Genome Campus 📅 11–14 Feb coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Our first lab paper is out. Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes. From single cells to patients, across tuberculosis and M. abscessus. 👉 doi.org/10.1038/s415... 👇 Thread

🫁 AIR 2026 registration closing 19th Jan Focused on respiratory infection, microbiomes and immunity, with amazing speakers. Incl genomics, single-cell, spatial and systems approaches. 📍 Wellcome Genome Campus 📅 11–14 Feb coursesandconferences.wellcomeconnectingscience.org/event/air-20...

It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...

new year, new job?! Exciting postdoc position opening in my lab at the Wellcome Sanger Institute. Fully funded by CRUK sanger.wd103.myworkdayjobs.com/en-US/Wellco... find out more at www.coelho-lab.com

We're organising a microbes & deep learning session at SMBE next year -- looking forward to seeing your abstracts!

Official Statement: Cambridge University, Department of Veterinary Medicine, 12/12/2025 "The decision to recommend the closure of what the Times Higher Education Supplement ranks as the best undergraduate veterinary course in the world has come as a bolt from the blue." [1] #SaveTheVetSchool

Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration! Feb 11th-13th, registration closing soon: coursesandconferences.wellcomeconnectingscience.org/event/air-20...

Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...

Great to share the latest work from our group and collaborators. First CARRIAGE study paper led by @drdaggarwal.bsky.social and the heroic efforts of Katie Bellis and Beth Blane in the lab plus all the team at @cambridge-ceu.bsky.social Huge thanks goes to the 22,000 participants of the study

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Abstract deadline now extended to Dec 1st. Lots of spots available for talks and posters. Great speakers and session with funders to discuss the future of respiratory research funding @eventswcs.bsky.social @microbiologysociety.org @asthmaandlung.org.uk @cysticfibrosis.org.uk Please share! 🫁

Really pleased to share the first paper to come out of the lab. We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung. The phylogenies indicate that the clones moved from lung->gut www.nature.com/articles/s41...

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

Abstract deadline now extended to Dec 1st. Lots of spots available for talks and posters. Great speakers and session with funders to discuss the future of respiratory research funding @eventswcs.bsky.social @microbiologysociety.org @asthmaandlung.org.uk @cysticfibrosis.org.uk Please share! 🫁

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

New 🧬✂️ pre-print! We show that paired prime editing can efficiently generate large deletions — even >1 Mb — with high precision and at scale. We use this to perform the first pooled prime deletion screen across the human genome. 🔗 biorxiv.org/content/10.1... A short thread (by Juliane Weller)👇

Showcase advances in infection and respiratory immunology at our 2026 conference! Share your insights on respiratory infection, host-microbiome interactions, and immune cell dynamics with field leaders. 🗓️ #AIR2026 dates: 11-13 February 📩 Submit an abstract by 17 November 📎 bit.ly/46T6uJB

Interested in respiratory infections? who isn't! Then register for this fab conference with a fantastic line-up of speakers and sessions @sangerinstitute.bsky.social Abstract submission open until 17th Nov!! @eventswcs.bsky.social coursesandconferences.wellcomeconnectingscience.org/event/air-20...

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers. 🚨 Submit your abstracts now! 🚨 Please RT coursesandconferences.wellcomeconnectingscience.org/event/air-20...

After being with the journal since its very inception, the time has come for me to step back from Microbial Genomics. This is a wonderful opportunity to have a leadership role in one of the leading journals for microbial genomics research microbiologysociety.org/news/society...

RIP Jane Goodall, by all accounts a wonderful woman who loved this Far Side cartoon

BBSRC Fellowships 2025 Triage Outcome Decisions were today. 277 applications, 42 put through to peer review and interview. A fellow I was supporting didn't get selected and BBSRC now offer *no feedback*. Months of work and not a single iota of feedback for the applicant. Honestly, disgraceful.

Proud to see my lab's work on M. tuberculosis and P. aeruginosa highlighted in this blog post

Now published, our tool to run (almost) all biological models interactively in your web browser Paper: academic.oup.com/bioinformati... Website: biomodels.bacpop.org Code: github.com/bacpop/SBMLt...

Synthetic lethal TN-seq! #microsky 🦠

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

It's that time of the year again... Soon the applications for 12 PhD positions at @sangerinstitute.bsky.social will open. Interested in genomics and thinking about doing a PhD? Join us at Sanger. www.sanger.ac.uk/about/study/...

Excited to share our @cp-cellhostmicrobe.bsky.social led by Magda showing how Bif has co-evolved with different animal hosts 🐒🐭🐷🐦 Key takeaways: 🔹 Host ancestry + diet shape Bif evolution 🔹 Mammals enriched for carb-busting enzymes 🔹 Untapped diversity in non-human hosts = new probiotic potential

Closing soon. Great opportunity to do spatial transcriptomics on pre-antibiotic TB

Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...