Sebastian Schmidt

YouTube video by Jimmy Kimmel Live Jimmy Kimmel is Back!

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.

Filtered hopes and full-spectrum realities

See also this perspective piece by Maria Vehreschild:

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

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...

Ig Nobel prize for study showing that drunk Germans speak Dutch better than sober ones Dutch Courage can help you speak a foreign language, according to a study by Dutch, English, and German researchers that was awarded an Ig Nobel prize on Thursday. They showed that alcohol consumption...

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 homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

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...

Reichstag Fire Decree - Wikipedia

In case you slept in history class:

en.wikipedia.org/wiki/Reichst...

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

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

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:

Disentangling the impact of obesity, diet, host factors, and microbiota on small intestinal antimicrobial peptide expression The small intestinal mucosa has the delicate task of allowing absorption of nutrients and limiting microbial colonization at the mucosal surface through production of antimicrobial peptides and pro...

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....

Lehrermangel: "Bitte tun Sie das nicht!!!" Wenn in Gelsenkirchen Lehrer fehlen, kann man doch welche aus Münster hinschicken, dachte die Behörde. Dann kam der Widerstand von Schülern, Eltern und Lehrkräften.

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...

YouTube video by The Tom Lehrer Wisdom Channel Tom Lehrer - We Will All Go Together When We Go - with intro

"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.

SPIRE: a Searchable, Planetary-scale mIcrobiome REsource Abstract. Meta’omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according

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 🖥️🧬🦠

Logo for the Sandpiper website

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 - Nature Biotechnology Novel microbial species in metagenomes are identified using conserved regions within universal marker genes.

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

Guilty as charged...

But also quite literally. I once put this as a biosketch into a talk:

Theory of host-microbe symbioses: Challenges and opportunities Growing insight into microbial symbioses highlights the need to model these systems mathematically. We discuss three areas requiring theoretical advan…

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...

Yes, that’s why we used the actual slope. We tested diff clustering cutoffs, 96.5% was (on avg) closest to 1:1, but we always use the marker gene-specific slope to convert cluster counts to species counts.

Agreed that reads contain (much) more information yet. But our premise was to ask: how much stuff do we assemble that does not make it into MAGs, but could given perfect binning & better seq depths? Reads give more diversity still, but assembled could be 'discovered' in MAGs in principle.