I’m hiring two postdocs to join my group at UCL, both funded for 3 years, to investigate how commensal bacteria contribute to the evolution and spread of antimicrobial resistance in pathogens. Please share! Links below 👇 www.jobs.ac.uk/job/DSU266/r... www.jobs.ac.uk/job/DSU268/r...

I’m at ECCB 2026 this week! I’ll be presenting my new eukaryote pangenome simulator, PansimNuc (github.com/samhorsfield...), at Poster C-G.38 on Wednesday 2nd September - drop by if you’re interested in modelling pangenome evolution! @eccb-europe.bsky.social

GitHub - samhorsfield96/PansimNuc: A nucleotide-level pangenome simulator.

A nucleotide-level pangenome simulator. Contribute to samhorsfield96/PansimNuc development by creating an account on GitHub.

github.com

📢 Deadline extended! The application deadline for our MOPITAS Autumn School on Spatial Transcriptomics Data Analysis, taking place October 12-14th in Copenhagen, has been pushed to August 16th. This is a great chance to sharpen your expertise in data science and multi-omics analysis. Register now!

Upcoming seminar: 🎓Professor Ari Molofsky @arimolofskylab.bsky.social, Tissue Immunology Research Lab, @ucsanfrancisco.bsky.social 📢‘Barrier immune niches during microbial colonization and infection’ 📅1-2 PM, Thu 16 July 📍Max Perutz Lecture Theatre, @mrclmb.ac.uk @cambridgebiocampus.bsky.social

Unfortunately, due to data storage restrictions, we have had to remove the individual SPIRE and mOTUs gene predictions datasets from HuggingFace. However, this data is still available in BacCorpus, with deduplicated gene predictions huggingface.co/collections/...

BacCorpus - a AllTheBacteria Collection

A dataset of diverse bacterial genomes across habitats. Includes deduplicated genomes, proteins and intergenic sequences.

huggingface.co

Happy to share the latest work from Zunair Khurram, a PhD student in our lab! Zunair has developed a new method, MxSure, to infer within-host substitution rates and transmission thresholds from longitudinal isolate and metagenomic sequencing data. www.biorxiv.org/content/10.6...

MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds

Quantifying short-term evolutionary rates of microbial genomes is essential for understanding the processes that shape within-host evolution and for establishing thresholds needed to track transmissio...

biorxiv.org

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!

Johanna von Wachsmann@johannavw.bsky.social · 3mo ago

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

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

PLOS Biology@plosbiology.org · 4mo ago

#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

#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...

agtools: a software framework to manipulate assembly graphs

AbstractMotivation. Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap info

academic.oup.com

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

Sam Horsfield@samuelhorsfield.bsky.social · 5mo ago

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...

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...

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…

sciencedirect.com

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...

Bacterial defense systems and host ecology drive the evolution of intra-species lineages

Staphylococcus aureus lineages vary widely in the frequency of gene exchange and the diversity of genome content. Gorzynski and Harling-Lee et al. show that both host ecology and the horizontal acquis...

cell.com

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-...

Description

Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

imperial.ac.uk

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

Danai Vagiaki@danaivagiaki.bsky.social · 8mo ago

Delighted to present Latent Interaction Variational Inference (LIVI), a framework for trans-eQTL mapping at single-cell resolution that I developed during my PhD together with colleagues from @steglelab.bsky.social 1/n

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.

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health

Silva et al. perform a global analysis of over 11,000 gut microbiomes and reveal that uncultured bacteria are key markers of gut health. The uncultured genus CAG-170 is strongly linked to low gut dysb...

cell.com

🎥 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

Sam Horsfield@samuelhorsfield.bsky.social · 8mo ago

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

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

Hugging Face – The AI community building the future.

We’re on a journey to advance and democratize artificial intelligence through open source and open science.

huggingface.co

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...

High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications

Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

nature.com

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

Wellcome Sanger Institute@sangerinstitute.bsky.social · 10mo ago

People who persistently carry the bacterium Staphylococcus aureus have a much less diverse community of bacteria in their nose, while certain species may help keep it out. 🦠 These findings offer insight into who may be at higher risk of infection. 👇 www.sanger.ac.uk/news_item/la...