We've been looking at how to compare and cluster large numbers of genomes, such as those in large isolate databases such as AllTheBacteria, and metagenome assemblies (e.g. SPIRE, MGnify). On a combined dataset of 5.6 million assemblies, we can now cluster/dereplicate everything in under a day!

Disrupting phage liquid crystalline droplets restores antibiotic susceptibility in Pseudomonas aeruginosa biofilms out in @plosbiology.org by @abultarafder.bsky.social and team. Exciting collaboration with @geiselbiofilm.bsky.social @pearce-maths.bsky.social and others

#Biofilm matrices containing filamentous phages help #Pseudomonas aeruginosa tolerate antibiotics. @abultarafder.bsky.social @tbharat-lab.bsky.social &co show that #nanobody disruption of #phage Pf4 #LiquidCrystalline droplets restores #antibiotic susceptibility @plosbiology.org 🧪 plos.io/4xkd6Mw

If you do any work with DNA sequencing at some point, you need to assemble the reads. Usually, we just use the contigs, but that ignores important evidence from your data, so @vijinim.bsky.social wrote agtools to explore the assembly graph and learn more! academic.oup.com/bioinformati...

New work on using transformers (using gene order) for tasks in genomic epidemiology: www.biorxiv.org/content/10.6... We trained BART models (w/ extended context windows) on E.coli and S.pneumo from AllTheBacteria and tested if the model could find new strains, insertions (blaCTX-M) and co-selection

Want to find #prophage in your #bacteria genomes? We built PhiSpy a long time ago, and now we've created a new web page for it: linsalrob.github.io/PhiSpyWeb/ Best of all, the data never leaves your computer! #phage #phagesky

Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...

We have two paid internships available in our group starting this summer, suitable for master's / pre-PhD students: - Protein structure search - Promoter variation For full details and how to apply see: www.bacpop.org/jobs/

Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....

Upcoming seminar: 🎓Professor Susanne Häußler, Head of Department of Molecular Bacteriology @helmholtzhzi.bsky.social 📢‘Functional Genomics in the Opportunistic Pathogen Pseudomonas aeruginosa’ 📅 4-5 PM, Thu 26 Mar 📍JCBC @cambridgebiocampus.bsky.social buff.ly/9PtbIn8 #CITIID

I did my PhD on bacterial meningitis, finding whether there are genetic factors which make meningitis more likely. Wrote down some initial thoughts on the current outbreak in Kent: johnlees.me/posts/menb-o... I tried to think of factors and their likelihood to explain why this is happening now

The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today: www.sciencedirect.com/science/arti...

Excited to share our latest paper c/w @jrpenades.bsky.social @jrossfitz.bsky.social et al! We found that S. aureus lineages have different pangenome structures driven by HGT, with horizontally-acquired defence systems (T1RM) being major drivers of lineage emergence 👇 www.cell.com/cell-reports...

Come join our team! Exciting opportunity for a clinical research fellow, ST1-ST7, to contribute to a novel Staphylococcus aureus human challenge model Deadline: 23 Feb 2026 Post start: up to Sept 2026 www.imperial.ac.uk/jobs/search-...

Working on trans-eQTL mapping with population-scale scRNA-seq? Meet LIVI, our latest framework that enables efficient trans-eQTL mapping at single-cell resolution across cohorts of hundreds to thousands of donors. Preprint: doi.org/10.64898/202... Summary in the 🧵 below by @danaivagiaki.bsky.social

Excited to share the newest paper from our team, where we uncovered a potential role of the uncultured gut #microbiome in health: www.cell.com/cell-host-mi.... Out now in @cp-cellhostmicrobe.bsky.social @cellpress.bsky.social. With Ana C. da Silva, Jacob Lapkin, Qi Yin and Efrat Muller.

🎥 Professor @andresfloto.bsky.social on new funding from: @wellcometrust.bsky.social @gatesfoundation.bsky.social @novonordisk.bsky.social and how VPD-HLRI research is helping reshape antibiotic discovery in the fight against antimicrobial resistance. Read more: 🔗 bit.ly/4rJy6c2

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

Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

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

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

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

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...

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

Bacteria can control what enters their cells, balancing energy and blocking antibiotics. New study in @natmicrobiol.nature.com uncovers this hidden mechanism of drug resistance: buff.ly/s3YIwyK @andresfloto.bsky.social @vpd-hlri.bsky.social @unibas.ch

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

Assembly, architecture and functional roles of microbial surface layers Review article published in @natrevmicro.nature.com with @bupbuse.bsky.social, Andriko von Kügelgen and @vikramalva.bsky.social. S-layers are everywhere! www.nature.com/articles/s41...

If you're interested in using pangenome graphs for comparative genomics, check out my webinar, part of EMBL-EBI's "Concepts, methods, and resources in pangenomics" series, available on-demand: www.ebi.ac.uk/training/eve...

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...

We are running a hackathon at EBI in Feb: biomics.bacpop.org If you are at EMBL, ETH Zurich, GRC or GIMM working on a biological problem in data science or programming, consider putting a project forwards!

To all my Pseudomonas aficionados: The 2026 International Pseudomonas Conference will take place on December 13-17, 2026 in Faridabad (close to New Delhi), India. Check it out! #microsky pseudomonas.io/home

🚀 As first official act, we are hiring! 🎓 We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded! More information here: www.bsc.es/join-us/job-...

A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

The EMBL PhD programme is open until 13th October (entry ~Sep 2026): www.embl.org/about/info/e... We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀 • 9× faster median speed vs bcftools • Higher accuracy for both SNPs & indels bioconda.github.io/recipes/quic... bmcbiol.biomedcentral.com/articles/10.... #microsky #microbiomesky

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

Thrilled to share our work is finally out at @natgenet.nature.com ! rdcu.be/eqGgf Combining a scalable human gut organoid model with TraDIS and statistical modeling, we mapped how Shigella colonizes the intestine at genome-wide resolution.

💥 Excited to introduce Bacformer 🦠 - the first foundation model for bacterial genomics. Bacformer represents genomes as sequences of ordered proteins, learning the “grammar” of how genes are arranged, interact and evolve. Preprint 📝: biorxiv.org/content/10.1... 🧵 1/n

Check out Maciek's tweetorial for Bacformer with links to code, tutorials and blog post: bsky.app/profile/macw...

New pre-print up introducing our bacterial protein language model Bacformer, creating a unified representation of entire bacterial genomes led by @macwiatrak.bsky.social www.biorxiv.org/content/10.1...

This year, our lab has a great representation at the ISMB/ECCB 2025 conference in Liverpool! Every day at the conference, you’ll have the chance to hear at least one talk or explore a poster by one of our incredible lab members. More details below. 👇

Defence Systems are so hot right now 🔥 🔥 🔥 so check out our latest preprint to see how DSes contribute to niche adaptation, interact with each other, and drive accessory genome interactions in Pseudomonas aeruginosa 1/n www.biorxiv.org/content/10.1...

Happy to share the first preprint from my lab. Great work by Lewis Fisher and collaboration with Jukka Corander www.biorxiv.org/content/10.1...

Please do take a look to see how @vpd-hlri.bsky.social’s @andresfloto.bsky.social, co-director of the Cambridge Centre for AI in Medicine, is using AI to improve health. www.cam.ac.uk/opinion-ai-a...

Great news Hayley! @thehjbrod.bsky.social and researchers at @camvetschool.bsky.social @julianparkhill.bsky.social Exciting research, giving us a better understanding of how the Streptococcus equi evolves and adapts, shaping the way it infects horses and donkeys. 👇🏽

Exciting PhD studentship opportunity in @andresfloto.bsky.social lab on understanding chemical permeability to advance antibiotic drug discovery www.jobs.cam.ac.uk/job/50800/. Combines experimental approaches with in silico screening and generative AI.

Tune into a Pseudomonas genomics webinar tomorrow at 11 UTC organised by @esgem-sg.bsky.social to hear me present our paper on the evolution of Pseudomonas aeruginosa www.science.org/doi/10.1126/... and talks from Adesola Olalekan and Sara Cortes Lara. Register here: us06web.zoom.us/webinar/regi...

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling