Aaron Weimann

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…

The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today:

www.sciencedirect.com/science/arti...

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...

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...

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...

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

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...

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

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.

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

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...

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 - Nature Reviews Microbiology Surface layers (S-layers) are ubiquitous protein assemblies that coat prokaryotic cells, with their functional roles increasingly coming into focus. In this Review, Isbilir and colleagues discuss rece...

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...

Metalog: curated and harmonised contextual data for global metagenomics samples Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data

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-...

BIOMICS hackathon at EMBL-EBI Hackathon held in Hinxton 2026

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

Fast and accurate variant identification tool for sequencing-based studies - BMC Biology Background Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, a...

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

Mathematical modelling for biologists - Modelling concepts in biological research Mathematical modelling for biologists - Modelling concepts in biological research

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

A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen Nature Genetics - A genome-wide screen using human gut epithelial organoids combined with transposon-directed insertion sequencing identifies over 100 Shigella flexneri genes required for...

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...

A contextualised protein language model reveals the functional syntax of bacterial evolution Bacteria have evolved a vast diversity of functions and behaviours which are currently incompletely understood and poorly predicted from DNA sequence alone. To understand the syntax of bacterial evolu...

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. 👇