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Sebastian Schmidt @tsbschm.bsky.social · 14d

Reposted by Sebastian Schmidt

Jimmy Kimmel @jimmykimmel.com · 14d

As I was saying…

Jimmy Kimmel is Back!

YouTube video by Jimmy Kimmel Live

youtu.be

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Reposted by Sebastian Schmidt

Mark Chadbourn @chadbourn.bsky.social · 15d

Psychologists everywhere frantically scribbling.

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Reposted by Sebastian Schmidt

Mark Chadbourn @chadbourn.bsky.social · 15d

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

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Sebastian Schmidt @tsbschm.bsky.social · 15d

See also this perspective piece by Maria Vehreschild:

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

Filtered hopes and full-spectrum realities

www.sciencedirect.com

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Sebastian Schmidt @tsbschm.bsky.social · 15d

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...

authors.elsevier.com

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Sebastian Schmidt @tsbschm.bsky.social · 16d

Scientific proof: Dutch is just drunk German.

nltimes.nl/2025/09/19/i...

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...

nltimes.nl

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Sebastian Schmidt @tsbschm.bsky.social · 16d

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

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 16d

The oral microbiome of King Richard III of England https://www.biorxiv.org/content/10.1101/2025.09.21.677585v1

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Sebastian Schmidt @tsbschm.bsky.social · 17d

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.

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Reposted by Sebastian Schmidt

Nature Methods @natmethods.nature.com · 20d

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...

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...

www.nature.com

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Reposted by Sebastian Schmidt

Luis Pedro Coelho @luispedrocoelho.bsky.social · 20d

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...

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Sebastian Schmidt @tsbschm.bsky.social · 20d

In case you slept in history class:

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

Reichstag Fire Decree - Wikipedia

en.wikipedia.org

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Sebastian Schmidt @tsbschm.bsky.social · 20d

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

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Reposted by Sebastian Schmidt

Pamela Ferretti @pamferretti.bsky.social · Aug 15

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

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Reposted by Sebastian Schmidt

Michael Kuhn @biocs.bsky.social · Aug 15

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

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...

www.biorxiv.org

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Reposted by Sebastian Schmidt

Michael Kuhn @biocs.bsky.social · Aug 15

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

Metalog

Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.

metalog.embl.de

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Reposted by Sebastian Schmidt

John F. Cryan @jfcryan.bsky.social · Aug 11

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...

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Sebastian Schmidt @tsbschm.bsky.social · Aug 5

Fun party game idea.

Guess the researcher based on G Scholar citation stats:

Reposted by Sebastian Schmidt

Bjo:rn Schro:der @mucubacter.bsky.social · Aug 5

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....

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...

www.tandfonline.com

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Sebastian Schmidt @tsbschm.bsky.social · Jul 28

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...

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.

www.zeit.de

Sebastian Schmidt @tsbschm.bsky.social · Jul 28

"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...

Tom Lehrer - We Will All Go Together When We Go - with intro

YouTube video by The Tom Lehrer Wisdom Channel

www.youtube.com

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Sebastian Schmidt @tsbschm.bsky.social · Jul 24

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.

Reposted by Sebastian Schmidt

Chan Yeong Kim @chanyeong-kim.bsky.social · Jul 21

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...

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

academic.oup.com

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Reposted by Sebastian Schmidt

Bork Group at EMBL Heidelberg @borklab.bsky.social · Jul 21

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 🖥️🧬🦠

Chan Yeong Kim @chanyeong-kim.bsky.social · Jul 21

Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...

www.biorxiv.org

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Reposted by Sebastian Schmidt

Ben J Woodcroft @benjwoodcroft.bsky.social · Jul 16

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 🧵

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