Sebastian Schmidt

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.

Plus SPIRE MAGs actually provide a significant chunk of the (incrementally added) species in GlobDB, so there's good overlap.

‪@daanspeth.bsky.social‬ kinda cross-posted the GlobDB preprint, we'll def include it in the next iteration!

Agreed. Note however that the 262k estimate is (i) just Bac and (ii) doesn't include ~half of GTDB r220 & proGenomes3. It's only "what is in the 90k metaG contigs considered".

It's quite interesting that ~50% of GTDB & PG3 genomes are *not* detectable in the contigs.

This is a view across marker genes when we go back with the inferred conversion factors (slopes) and re-predict species counts. Y axis is deviation (1 - rho).

NB: `spire.species` are GTDB classifications (only) for SPIRE MAGs, `spire.ani` is just 95% clusters of SPIRE MAGs as a "species" equiv.

@benjwoodcroft.bsky.social so this is an example for a (random) archaeal marker. X axis is n of clusters, y axis is n of species; it's rarefied based on n of genomes considered. It's quite linear and quite close to slope=1 (give or take across markers).

It’s one fit per marker gene, per reference set - so not 100k species, but smaller sets (like all arc/bac in progenomes, in GTDB, etc). I’ll dig up the plots later.

I think you need tools like Bin Chicken to actually get MAGs there ;-)

Hard to know what this clade eg is. We‘re just confident after checking what it’s not: virus, euk nor bacteria.

Point taken, but link is in the quote-skeeted quote-skeet.

Quote-skeet-ception at this point, admittedly…

In fact, this is unironically my favourite way to start a Monday. To start most days actually.

(My wife’s a dentist though, I may be biased)

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?"

Finally, thanks to all other co-authors: A Fullam, @ecekartal.bsky.social‬ , @pangenomics.bsky.social , @luispedrocoelho.bsky.social , A Spang & @borklab.bsky.social

And of course to the lead authors @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social

A census of hidden and discoverable microbial diversity beyond genome-centric approaches Cataloguing Earth's biodiversity remains one of biology's most formidable challenges, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing census of...

There are many more stories in the preprint, so go ahead and read it:

www.biorxiv.org/content/10.1...

We welcome feedback!

We estimate that ~10 novel archaeal and ~145 bacterial phyla are "hiding" among the unbinned contigs. This corresponds to an increase of ~50% and ~83% relative to ref dbs.

For genera, we find that >3 novel genera are discoverable per each recognized genus in the reference.

Finally, we built >130 large marker gene phylogenies and cut them at relative evolutionary divergence (RED) levels corresponding to phylum-, class-, order-, family- and genus-level clades.

(dots in the plot below indicate phyla and families)

This becomes even clearer in an "incremental" rarefaction analysis. Although human-assoc and gut samples account for >2/3 of samples in the survey, they only contribute 1/3 of total discovered diversity.

Most unbinned species species lurk among soil, aquatic & wetland samples.

Given SPIRE's curated sample annotations, we broke these numbers down by habitat. We calcualted a 'species discovery coefficient' α.

Few habitats show signes of saturation (no new sp. added as more samples come in, α≤0). Most, in particular soils & aquatic envs, remain in full discovery swing.