Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1

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

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

Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/

Really excited to announce the v1.9 release of the `rich-click` library 🎉 It's a Python library that uses builds on top of command-line help output from click, giving you beautiful output with only a couple of lines of code 🪄 ✨ 🌈 v1.9 TLDR: We have themes!

Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!

Introducing AMR cartography - work by Andrew Balmer

🚨 An excellent opportunity for scientists in Africa, at all career stages, working on maternal & child microbiome research 🚨 📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring. coursesandconferences.wellcomeconnectingscience.org/event/human-...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀 • 11–24× fewer suboptimal alignments (same for human genome) • 3–579× lower inconsistency • improves on ~30% of reads aligned to non-target species github.com/mathjeff/map... bioconda.github.io/recipes/x-ma... #microsky

Sometimes you meet absolutely incredible bioinfo-magicians. It was a huge privilege when @shenwei356.bsky.social joined our group for a year on an @embl.org sabbatical. While here, he developed a new way of aligning to millions of bacteria, called LexicMap 1/n www.nature.com/articles/s41...

The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...

Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills. Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org 🧬💻

This study describes the oldest microbial DNA ever sequenced go.nature.com/4nfIzcU

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

New blog post: Using OpenAI Codex in @posit.co Positron with a demo on developing an #Rstats package using the OpenAI Codex agent doi.org/10.59350/ste...

A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species go.nature.com/4fFfx3F

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 cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1

If ever a species needed a large scale long-read genomics project it is Y. pestis. Great paper! www.nature.com/articles/s41...

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

New from The Strain Team: 🎊 Springer Nature Discovers MDPI 🎊 Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗). Gross! 😀 1/n #ResearchIntegrity #SciPub #AcademicSky

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

Myself and @yekwah.bsky.social are running our bacterial AMR databases and genotype prediction course again with @eventswcs.bsky.social. Completely free and study at your own pace. Check out the course objectives below and sign up before June 9th to join us! www.futurelearn.com/courses/anti...

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

Excited to share the first beta release of AMRrules at #ABPHM! (Poster 42 tonight) interpretamr.github.io/AMRrules

We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July www.training.cam.ac.uk/bioinformati... Please let anyone who may be interested know.

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

🥁 NEW: Commentary in @cellcellpress.bsky.social! by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger www.cell.com/cell/fulltex... 1/4

www.biorxiv.org/content/10.1... Autocycler, the automated successor to Trycycler from @rrwick.bsky.social has a pre-print out - overall, pretty awesome performance (and is very easy to use) github.com/rrwick/Autoc...

Wonder the "chemicals" between gut bug pairs? Check out this new preprint lead by @skamrad.bsky.social and am honored to contribute!

New opinion paper from the lab! www.cell.com/trends/micro...

Excited to launch "ggplot2 [un]charted" with @yan-holtz.bsky.social! 🎉 An online course to master #ggplot2 with exercises, quizzes, and modules—and hands-on code running in your browser! Still WIP—sign up now for a limited discount: 👉 www.ggplot2-uncharted.com #rstats #DataViz #DataVisualization

🚨 Teaching bioinformatics? Or learning it solo? Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required. 🔬🧬👩‍💻 📚 github.com/lskatz/funda... ⭐️ Star it, share it, and level up! #bioinformatics #opensource #STEMeducation

With {tidylog}, you see friendly messages like: summarise: now 3 rows and 3 columns, ungrouped filter: removed 2 rows (67%), one row remaining ✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!

www.biorxiv.org/content/10.1... Searching for lytic phages in bacterial genome assemblies ..!

You have until 25 May to apply for this @embo.org Practical Course introducing concepts, methods and tools for carrying out infectious disease modelling using genomics www.ebi.ac.uk/training/eve... There is some financial assistance provided by EMBO - please see the course website for info 🧪🧬🖥️🦠🧫

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...

Out now in Cell! Thrilled to share our recent study on global analysis of microbial genetic diversity in geography and human health. Congrats @seandreu.bsky.social and all other co-authors. Special thanks go to @cibiocm.bsky.social and lifelines.

Small update from AllTheBacteria (allthebacteria.org). Assemblies can be bulk downloaded from OSF as before, or you can now get individual assemblies from AWS. We now also have a LexicMap index on AWS, so you can align your favourite gene against 2.4million bacteria (next post for price estimates)

Aww look at these trend setters in #microbiology! Interested in the large genome structural variation that isn't accounted for in short read #sequencing & consequences these have, read the latest review by our @emmabeansworth.bsky.social & @gemma-langridge.bsky.social #academicsky #academicchatter

New work in Nature shows that a brief 5-day CIP course in (n=60) healthy adults can lead to emergence of AMR in ~10% of ~5600 gut microbial species. Most mutations in gyrA (known FQ hotspots), do not affect fitness & can be detected >10wks (projected to persist >1y) 🔗 www.nature.com/articles/s41...

SeroBA(v2.0) and SeroBAnk: a robust genome-based serotyping scheme and comprehensive atlas of capsular diversity in Streptococcus pneumoniae https://www.biorxiv.org/content/10.1101/2025.04.16.648953v1

argNorm is published now academic.oup.com/bioinformati...

Our latest preprint is out describing amr.watch - a platform for monitoring AMR trends from global genomics data: www.biorxiv.org/content/10.1... (1/6)

bioinformatician, computer scientist, and geneticist lead bioinformatic tool development—which one is better? academic.oup.com/bioinformati...

New Preprint klaxon - and calling all Danes+Brits who are interested in genetics+history - a new preprint led by Xiaolei Zhang in my group with Soren Brunak's group about genetic exchange from 1100 to the present day between UK (Britain)+Denmark. Read on for details www.biorxiv.org/content/10.1...

#MicroSky #AMR

We published a cool new paper showing that some M tuberculosis lineages (mainly L1 and L6) seem less transmissible but that's mainly because they have longer initial non-infectious 'latent' periods. www.sciencedirect.com/science/arti...

Another week and more pipeline updates, this time my two assembly pipelines: Illumina: github.com/avantonder/a... ONT: github.com/avantonder/a... Have a try and let me know what you think

If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc: sanger.wd103.myworkdayjobs.com/WellcomeSang... Incredibly exciting datasets on host-microbe interactions in the lung. Pls RT and reach out if you are interested.