Sebastian Schmidt

GlobDB: a comprehensive species-dereplicated microbial genome resource AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...

The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published!

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

🚨Job claxon 🚨

University College Cork is looking to appoint a lecturer in Medical Microbiology into a permanent, non-clinical post

A great opportunity in a microbiology powerhouse

For details go to my.corehr.com/pls/uccrecru... and enter reference number 092153

There are several additional stories and refinements in the updated preprint, e.g. on possible reasons why some lineages remain unbinned (might have to do with GC content).

We have received thoughtful (and critical) feedback on the initial version and look forward to receiving more!

This means that biodiversity likely follows consistent patterns across the Tree of Life, with power law clade size distributions spanning multiple orders of magnitude.

If you spin this further, this supports the idea of fractal geometries in the Tree of Life.

We also compared to data for eukaryotes (from @gbif.org ) or prok from other dbs ( @ace-gtdb.bsky.social and microbeatlas.org) which showed similar curves, with surprisingly consistent estimates of ρ coefficients.

Similarly, species-rich phyla were dominated by large clades (low ρ), but w/ interesting outliers such as Patescibacteria.

ρ varied across habitats.

While deeper sampled habitats had lower ρ (as expected), there were interesting deviations from the trend: hot springs harbour more small clades than expected, the oral cavity is disproportionately dominated by large clades.

The Yule-Simon coefficient ρ can be thought of as a 'rich get richer' parameter: lower ρ indicate distributions more dominated by large clades (i.e., stronger 'preferential attachment' patterns); higher ρ means a higher fraction of small (singleton, doubleton) clades.

We tested these ideas on our large set of (data-driven and agnostically inferred) prokaryotic clades, and lo and behold: they follow Yule-Simon distributions, across taxonomic levels (from species per genus to classes per phylum).

x axis in plot is 'clade size' (i.e., n of subclades)

Yule (royalsocietypublishing.org/doi/10.1098/...) used these observations to develop his seminal theory on how novel clades arise preferentially within existing large clades. Mathematically, distributions resulting from a Yule process deviate from 'naïve' power law curves.

>100 years ago, Willis (www.nature.com/articles/109...) famously observed that genus size distributions (n of species per genus) follow power laws in plants and animals, in what he called 'hollow curves'.

We now dug deeper and studied diversity patterns beyond total counts of discoverable lineages: we asked whether *clade size distributions* follow consistent patterns across the Tree of Life.

The main story are estimates of 'discoverable' species, genera, ..., phyla (?) in unbinned metagenomic contigs that do are not captured by MAGs. How many lineages lurk in existing data, and which habitats are prime hotspots for the discovery of novel diversity?

Original 🧵:

bsky.app/profile/tsbs...

Hidden but discoverable diversity in the global microbiome Cataloguing Earth's biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing cens...

We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social

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

Tja…

Agreed! There is a history of similar benchmark studies both on wetlab and drylab microbiomics though. I am more discouraged that this kind of study is still necessary (and produces such results) in 2025…

Yes of course. I was specifically referring to the drylab side of things, but for the wetlab side protocols have been benchmarked ad nauseam as well and still some of the demonstrably bad kits and bad protocols remain popular.

This is, unfortunately, not surprising at all. There is huge variability on both the wet and dry lab side. Benchmarks like CAMI exist and show that accurate tools exist, but having good tools is useless if ppl prefer to use the ones with fancy website and powerful lobby instead.

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

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

Logo of Bin Chicken (Australian white ibis) on a rubbish bin, pulling out a strand of DNA

“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

also, we were focussing on ONT data (+ Illumina) in this case.

List of longread studies

I made this list some time ago. It is not complete though.

docs.google.com/spreadsheets...

From the musicaljenga community on Reddit: Ballroom Jenga (guitar + drums added) Explore this post and more from the musicaljenga community

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.

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

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-...

The manuscript is in press, so… soon :-)

Together, these dbs allow one to address 'big' questions in microbial ecology & evolution with 'big' data, at unprecedented scales.

Give it a try, and feedback is always welcome!