(They can be fetched from there while some server issues in the background are being fixed)

GUNC pre-processed databases are now also on zenodo thanks to @fullam.bsky.social :

zenodo.org/records/1963...

This is bad.

Personally, I maintain that if a study does not release data, it should be considered not on the scientific record and can therefore be ignored. To restrict, you need very strong (exceptional) reasons.

Predictably, that's not a popular stance with many though.

Due to some IT problems, the Bork group homepage and various services such as SPIRE and Metalog are unfortunately going to be unavailable for a couple of days. We're sorry for that and hope that the outage can soon be resolved!

Bioinformaticians all over the world:

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

@fullam.bsky.social has given the SPIRE website a bit of an overhaul: improved pages, nice new options to navigate, improved search, streamlined genome, study and sample pages, tidied up Downloads page, etc.

Go check it out:

spire.embl.de

@tkorem.bsky.social another comment/suggestion: we noticed differences in an inconspicuous step of pipelines – mapping & coverage quantification.

We tested bwa-mem2, fairy (by @jimshaw.bsky.social ) and aemb (www.biorxiv.org/content/10.1...) and the impact on accuracy is notable.

I’m also surprised by this. We (less systematically) tested metabat2 and semibin2 for multi vs single binning on a bunch of samples and both recall and precision were consistently better for multi binning. Afaik @luispedrocoelho.bsky.social & team looked into this deeply as well.

It’s also encouraging to see that much of this aligns with our pipeline updates for the next version of SPIRE which we vibe-benchmarked based on much less sophisticated tests and setups.

This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through!

www.biorxiv.org/content/10.6...

Would the best solution not be to involve the orig tool's authors? I think it's in everyone's interest to ideally streamline legacy spaghetti code from non-dev scientists (like me, I speak from experience), but why not communicate with and invite contributions from orig authors?

Finally, on behalf of all authors I want to thank peer reviewers @acritschristoph.bsky.social , @mattolm.bsky.social and Don Cowan (U Pretoria) for their thoughtful and constructive feedback. Review history is online; you can read how their comments really helped us improve our study!

This is also a special and somewhat strange, bittersweet moment. It's the first major study from my own team, but it is also based on early discussions and collaboration with my former supervisor Peer Bork – published after he recently passed away.

I will write more after the Easter break, but for now congratulations to @vishnuprasoodanan.bsky.social @omaistrenko.bsky.social and all other co-authors (including @fullam.bsky.social @pangenomics.bsky.social @luispedrocoelho.bsky.social @anja1.bsky.social )!

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :

www.nature.com/articles/s41...

See the linked threads for more details!

MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies.

A new paper in 𝐂𝐞𝐥𝐥 presents MicrobeAtlas, a harmonised resource built from more than 2 million microbiome samples. It reveals recurring community patterns, geographic preferences and broad trends across microbial ecosystems. Congrats to @tsbschm.bsky.social #Microbiome #microsky
📰 buff.ly/PsNS9ML

Antimatter has been transported for the first time ever — in the back of CERN’s truck Physicists have succeeded for the first time in transporting the most expensive and most volatile substance on Earth: antimatter.

Wait I think I've seen this movie. Just don't let Ewan McGregor get anywhere near it...

www.nature.com/articles/d41...

Well, not on purpose, rather with sheer weaponized incompetence.

They're welcome to using my code because then future Copilot will do incredibly stupid things.

Urban soils are a small part of the world and lack the glamour of the wilderness or the economic importance of agriculture, but as most people live in cities, they are very important

Our latest preprint using long-read metagenomics reveals massive hidden diversity and function in city soils

🧵

New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows.

We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠

Here's what we found 👇
doi.org/10.1128/msystems.01062-25

I think the calculation breaks down for many tools at <90%. mash and skani become much less precise there.

That said, the best reference for this imo is not ANI, but RED relative to the GTDB ref tree (you can look up the thresholds in their docs).

AlphaFold database has entered the era of complexes. Together with NVIDIA, DeepMind and EBI, we use ColabFold, OpenFold and MMseqs2-GPU to predict ~31 million complexes (homo & hetro-dimers) resulting in 1.8 million high-quality predictions
📄 research.nvidia.com/labs/dbr/ass...
🌐 alphafold.ebi.ac.uk

@fullam.bsky.social has pushed a new #GUNC release, v1.1.0:

github.com/grp-bork/gun...

It fixes some bugs, updates some underlying databases and brings new features (e.g. you can now BYODB – bring your own database).

GUNC v1.1.0 is also live on #bioconda .

@fullam.bsky.social has pushed a new #GUNC release, v1.1.0:

github.com/grp-bork/gun...

It fixes some bugs, updates some underlying databases and brings new features (e.g. you can now BYODB – bring your own database).

GUNC v1.1.0 is also live on #bioconda .

Proposed signalling pathway of the aged microbiome impairing cognition through increased MCFA production leading to peripheral inflammation, vagal impairment, and cognitive deficits.

A new study in @nature.com reveals how changes in gut microbes during ageing can disrupt communication between the gut and brain, contributing to cognitive decline.

Huge congrats to APC collaborators Adrián Cortés-Martín and Colin Hill

Read the paper: buff.ly/EYAjYgE

#Microbiome #BrainHealth

As an UZH alumnus, I take offence. The cuckoo clock is clearly from the Black Forest.

The Swiss famously claim credit for all that is good in the world ("Wer hat's erfunden?"). In many cases rightly so.

Congratulations, Lisa Maier and Stephen Cusack!

The two EMBL alumni have received the 2026 John Kendrew and Lennart Philipson awards for their outstanding contributions to host–microbiome research and structure-guided drug development, respectively.

Learn more: www.embl.org/news/awards-...