#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

The world is a much better place because r/musicaljenga exists. www.reddit.com/r/musicaljen...

IYKYK...

Its a pretty safe bet that Donald Trump will be in the official champions photo after the World Cup 2026 final, standing in first line and holding the trophy.

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-...

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-...

"As a scientist, how do you feel about the US Secretary of Health?"

🫣

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

ICE footage from the US is just shocking. As a German it hits particularly hard because they act like the SS and SA did in 1930s Nazi Germany. And I have been asked countless times, "why did regular people not stand up to the Nazis". Never thought we'd one day have to ask Americans the same thing.

“It’s more of a comment than a question…”

As I was saying…

Psychologists everywhere frantically scribbling.

I don’t think I’ve ever seen America so embarrassed in front of the entire world.

Fecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social . Congratulations to Dina Kao @ualberta.bsky.social & team! Gift link: authors.elsevier.com/c/1lphg8nByr...

Scientific proof: Dutch is just drunk German. nltimes.nl/2025/09/19/i...

A toothbrush! A toothbrush! My kingdom for a toothbrush!

Miller giving Sportpalast vibes… Dear USA, we’ve been through all this 80-90 years ago and really 0/10, can’t recommend. Regards, Germany.

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

Seems like the death of Charlie Kirk is really turning into the USA's Reichstagsbrand moment.

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠 Proud to have contributed to Metalog, the latest @borklab.bsky.social resource: www.biorxiv.org/content/10.1... #microsky #microbiome

We hope many of you will find it useful, and will continue to add data. Here's the preprint: www.biorxiv.org/content/10.1... - hopefully coming soon to a NAR Database Issue near you 😅 Thanks to everyone in the @borklab.bsky.social @embl.org who contributed to this! 7/7

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

Putting the Global South on the Microbiome research map - Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in ‪@natcomms.nature.com‬ "If microbiome science is to benefit everyone, it must include everyone." www.nature.com/articles/s41...

Fun party game idea. Guess the researcher based on G Scholar citation stats:

Our study on disentangling the impact of #obesity, #diet, host factors, and #microbiota on small intestinal #antimicrobialpeptide expression is now published in Gut Microbes! Fantastic work by Fabiola Puértolas-Balint et al! #microbiomesky #microsky #GastroSky www.tandfonline.com/doi/full/10....

Ich bin in Gelsenkirchen geboren und habe dort Abitur gemacht. Dieser Artikel macht mich unendlich wütend und traurig. Und leider entspricht das Geschilderte komplett meinen Erfahrungen mit Münsterländern und verbeamteten Lehrer*innen. www.zeit.de/2025/31/lehr...

"We will all go together when we go." Well, Tom Lehrer is gone now and maybe he wasn't wrong after all. Unrelated, the collective sigh of relief from the New England pigeon population was audible this side of the Atlantic. www.youtube.com/watch?v=TIoB...

As a German, I've often wondered what 1933/34 must have felt like for people outside Germany. Now I'd rather not have found out.

The metagenomic datasets used in this study are from SPIRE. academic.oup.com/nar/article/... If you are interested in the planetary microbiome, see also recent MicrobeAtlas preprint from von Mering group: www.biorxiv.org/content/10.1...

New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details! #MicroSky 🖥️🧬🦠

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs

Our article on the challenges and opportunities in studying host-microbe symbioses is now published in Cell Host & Microbe! @cp-cellhostmicrobe.bsky.social www.sciencedirect.com/science/arti...

Our preprint on estimating how many more prokaryotic taxa can be discovered in the unbinned fraction of metagenomic samples. We predict that there are 10 archaeal and 145 bacterial novel phyla across all habitats. #MicrobialDarkMatter #TreeOfLife #Microbiome #Archaea #Bacteria #Metagenomics

Quick thread on the WHO's SAGO report on the origins of COVID-19, highlighting key points and even *new* data. Their summary is that a zoonotic origin of COVID-19 is best supported by available data. This is consistent with most scientific reviews and statements in the rest of the literature.

New Preprint Alert! 🌍🧬 We’re thrilled to share our latest study tackling one of the biggest question.. "How many prokaryotic species, genera, and deeper lineages actually exist on Earth?"

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

When yet another 16S-based paper discusses analyses of “strains”.

That is not OK. I hope that call will be reversed, as such things should not happen in science.

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896 If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.

Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field. rdcu.be/epoRR @blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.

The Koonin Law of Computatoinal Biology: Whenever you think you have a great idea in computational or evolutionary biology, it will already have been published by Eugene Koonin in the mid 90ies.

Archaea xkcd.com/3095/

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

Same energy. #IYKYK

A 1.0 release for Sandpiper. 700,000 microbial community profiles (3x the last version, 4.7 Pbp metaG), searchable via the @ace-gtdb.bsky.social R226 taxonomy that just dropped. MetaGs are going exponential, but we are still nowhere near a MAG for all species. sandpiper.qut.edu.au #microsky 🧬🖥️ 1/2