Thank you Jacob!

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉

How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬
www.nature.com/articles/s41...

Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social

www.nature.com/articles/s41...

Great team effort and pleasure to write this review with @ettema.bsky.social @micropat.bsky.social @stephkoe.bsky.social @gerbenz.bsky.social

Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...

Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives.
www.nature.com/articles/s41...

Beyond thrilled to share that our study has been published!
This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and
@texasscience.bsky.social!!!
#MicroSky #ArchaeaSky 1/12

New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...

Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...

Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41...

Corrected paper: www.nature.com/articles/s41...

Importantly, the re-analyses of the corrected dataset are consistent with the original findings.

a man walking in a field with an umbrella ALT: a man walking in a field with an umbrella

Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea

21 Vidi grants awarded to Utrecht-based researchers 21 researchers from Utrecht University, University Medical Center Utrecht, and Princess Máxima Center have each been awarded a Vidi grant worth up to €850,000.

Exultant to have been awarded a Vidi grant by the Dutch Research Council (NWO)! Can't wait to get started!

Stay tuned for two upcoming (PhD student & postdoc) positions to study archaeal genome evolution.

Also huge congrats to my colleague @dorotakawa.bsky.social!

www.uu.nl/en/news/21-v...

academic.oup.com/mbe/advance-...

Happy to share this one. We investigated the #phylogenetic placement and #genome_evolution of Pangui/Njordarchaea-unique #Asgardarchaea that might have undergone genome reduction...

GitHub - stephkoest/witchi: A compositional bias testing and pruning tool for multiple sequence alignments A compositional bias testing and pruning tool for multiple sequence alignments - stephkoest/witchi

Check out this beautiful work led by @stephkoe.bsky.social, with great teamwork from @danieltamarit.bsky.social and @ettema.bsky.social :
💻 github.com/stephkoest/w...
📄 doi.org/10.1101/2025.07.14.663642

🧂The placement of halophilic lineages was restored — Methanonatronarchaeia emerged outside Halobacteria, supporting independent origins of halophily
(in agreement with targeted analyses: doi.org/10.1038/s415... &
doi.org/10.1038/s415...)

🧩 Phyla representing the clades Acherontia and Stygia (Methanobacteriota_B + Hadarchaeota) shifted to sister TACK + Asgardarchaeota — consistent with site-heterogeneous models (doi.org/10.1186/s128...).

Among the topological improvements:

🔥Thermophilic clades (e.g. JANJXX01, DRAE01, Korarchaeia) were repositioned in line with recent phylogenomic studies (doi.org/10.1038/s415... &
doi.org/10.1101/2025...).

→ The number of biased taxa dropped from 95.1% to just 2.3%
→ Pruning automatically stopped once further trimming risked loss of phylogenetic signal

Discrepancy between observed and expected amino acid frequencies in taxa:

Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.

The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes.

🔗: doi.org/10.1016/j.ce...

#Genomics #Evolution #CellBiology #LECA

Our review on how thermophilic carbon monoxide(!)-eating microbes can aid the transition to renewable carbon-based products.

Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focus...

#Asgard,#phylogeny
1/ 🧵 Does MAGs contamination affect the placement of Njord as suggested by Zhang et al, 2025? www.nature.com/articles/s41...
Our updated analysis suggests instead... www.biorxiv.org/content/10.1...

New vacancy in my team!

PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture.

Please repost and share with talented MSc students in #evobio, bioinformatics or related :)

www.uu.nl/en/organisat...

#MEvoSky #MicroSky

Ectomycorrhizal symbiosis evolved independently and by convergent gene duplication in rosid lineages Click on the article title to read more.

Excited to share our recent work on the evolution of ectomycorrhizal plants! 🌳 🧬 🖥️
doi.org/10.1111/nph.70054

With: Yvet Boele, @puginiercamille.bsky.social, @mbianc.bsky.social, Cyril Libourel, @maximebonhomme.bsky.social, @kellerjeanphd.bsky.social, @pierremarcdelaux.bsky.social

A thread: (1/5)

Postdoc Comparative genomics and genome architecture in early-diverging fungi and their protist relatives (3-year position)

Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...

Ettema Lab Wageningen Join the conversation

Not new here but will become more active at @bsky.app (I am no longer active on X)

Follow me to hear more about the wonderful world of microbes (evolution, archaea, symbiosis, new microbes, ...). Expect occasional rants about academia, 🇳🇱 politics, life, etc.

My research group: go.bsky.app/MzZPftE