Gut bacteria form #spores, but our lab models rarely match the real thing. A new review in @cp-trendsmicrobiol.bsky.social argues for developing model organisms from human gut spore‑formers. Current models miss key genetics & biology of Bacillota species common in people. 📰 buff.ly/ZWLKobR

Reposting this from April 1, 2007 in honor of Craig Venter. I did this as an April Fool's joke - sharing it as a PDF. I got stressed when I found out Craig had seen it and knew it was by me. But he loved it and said it was OK to share it more widely. So then I posted it on the web.

Indeed.. here is "generate the first page of a great Nature paper that will get lots of citations. It must be very novel."

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

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...

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!

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

Wait I think I've seen this movie. Just don't let Ewan McGregor get anywhere near it... www.nature.com/articles/d41...

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

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 .

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

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-...

No, your "AI platform for scientific profiles" got this one quite wrong I'm afraid. Wouldn't say no to "227+" publications, but I draw the line at being called an expert in Diarrhea.

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

MicrobeAtlas is now published in Cell. 🌐🌎🦠 Explore the paper and resource to see what large-scale microbiome data reveal about global ecological patterns: www.cell.com/cell/fulltex... For a concrete application, see our recent work on “Community conservatism”: www.nature.com/articles/s41...

Has anyone been able to figure out who that "Companion AI" company behind this Einstein Canvas completion bot is? They don't really seem to have an online footprint at all, no legal address on the website, nothing.

As a fervent Discworld fan, this one hits hard.

This graph gives me nightmares (but in a good way)

me: trust me, there's so much cool stuff we can to with SPIRE data! half the ppl I say that to: nah, it's a nice resource, but I just don't see it. me: *gestures wildly at @chanyeong-kim.bsky.social & @podlesny.bsky.social 's new study now out in @cellpress.bsky.social *

In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠 🔗 Read more here: www.embl.org/news/science...

Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!

I invite you to check our paper entitled “Rebuilding Ukraine’s capacity for fundamental research in evolutionary biology” doi.org/10.1038/s415... in @natecoevo.nature.com about the Ukrainian School in Evolutionary Biology #USEB we organized in 2025. #biology #evolution #school #science #Ukraine

From Fork to Feelings: How Foods Shape Mental Health via the Microbiota–Gut–Brain Axis Latest review out in @annualreviews.bsky.social -Well done Aimone Ferri, Laise Paes & @elizschneider.bsky.social www.annualreviews.org/content/jour... @apcmicrobiomeirel.bsky.social @anatneuroucc.bsky.social

Aber Hauptsache, wir lassen Homöopathie, Akkupunktur und Ayurveda im Leistungskatalog... www.zeit.de/politik/deut...

It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵

APC & @teagasc.bksy.social are recruiting a Postdoctoral Research Fellow to analyse gut microbiome datasets and the impact of birth mode and antibiotic exposure. Bioinformatics experience required. #microbiome #jobfairy #researchjobs #metagenomics Full Details: bit.ly/4qQgRWr

FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...

prodigal has entered the chat.

I have been one of the many people across the world impacted by the sudden death of Peer Bork - a friend, colleague and remarkable scientist. I now have enough time this weekend to write some personal thoughts about Peer. www.linkedin.com/posts/ewan-b...

very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...

Sad day. @borklab.bsky.social bring so much to Science and notably in the #microbiome RIP Peer thank you for all your legacy. www.embl.org/news/embl-an...

This is such an elegant study. Great to see it published!

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...

Finally.

Hands down one of the best sentences ever written in a scientific Abstract. And in @nature.com no less... www.nature.com/articles/s41...

My heart goes out to the people of Iran tonight.

What if Trump's and Miller's current antics around Greenland are just a devious and elaborate PR stunt to promote an upcoming Gerard Butler movie

This is, quite literally, Putin's playbook for Russia since around the year 2000.

Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below

Three decades of biodiversity data, published one decade after we started the project! Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years. www.nature.com/articles/s41...

This is amazing. I once sang the „original“ (Chant des Oiseaux) with an 8 voice a Capella ensemble and this is still one of my fondest choral memories!