Stephan Köstlbacher
@stephkoe.bsky.social
Former PostDoc at Wageningen University with Thijs Ettema
Studying ancient evolutionary transitions in prokaryotes using phylogenomics and structural modeling
Looking for next step in academic or translational research
he/him
Studying ancient evolutionary transitions in prokaryotes using phylogenomics and structural modeling
Looking for next step in academic or translational research
he/him
Pinned
Stephan Köstlbacher
@stephkoe.bsky.social
· Jul 20
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
www.biorxiv.org
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
Reposted by Stephan Köstlbacher
Reposted by Stephan Köstlbacher
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages https://www.biorxiv.org/content/10.1101/2025.11.11.687807v1
November 12, 2025 at 11:32 PM
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages https://www.biorxiv.org/content/10.1101/2025.11.11.687807v1
Reposted by Stephan Köstlbacher
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
November 12, 2025 at 9:50 AM
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
🧙♀️ Something is brewing in the WitChi cauldron…
After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments.
Stay tuned for the next release!
🧙♀️ Can’t model it? Prune it!
github.com/stephkoest/w...
After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments.
Stay tuned for the next release!
🧙♀️ Can’t model it? Prune it!
github.com/stephkoest/w...
October 31, 2025 at 9:59 AM
🧙♀️ Something is brewing in the WitChi cauldron…
After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments.
Stay tuned for the next release!
🧙♀️ Can’t model it? Prune it!
github.com/stephkoest/w...
After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments.
Stay tuned for the next release!
🧙♀️ Can’t model it? Prune it!
github.com/stephkoest/w...
Reposted by Stephan Köstlbacher
Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky
Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution
Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.
www.nature.com
October 21, 2025 at 3:06 PM
Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky
🧵 Our study on the elusive titration control mechanism of the replication initiator DnaA in Escherichia coli is now out on @natcomms.nature.com! @stephkoe.bsky.social
@hohlbeinlab.bsky.social @nicoc-micsynmet.bsky.social @ettema.bsky.social @mib-wur.bsky.social
doi.org/10.1038/s414...
@hohlbeinlab.bsky.social @nicoc-micsynmet.bsky.social @ettema.bsky.social @mib-wur.bsky.social
doi.org/10.1038/s414...
The Escherichia coli replication initiator DnaA is titrated on the chromosome - Nature Communications
A DNA-binding protein, DnaA, regulates the initiation of chromosomal replication in bacteria. Here, Olivi et al. show that the bacterial chromosome sequesters DnaA in a growth rate-dependent manner, s...
doi.org
August 22, 2025 at 9:30 AM
Never thought I’d do real E. coli research, so far I used if only for cloning & protist snacks in my MSc 😅
But here I am simulating chromosomes & shuffling motifs.
Watching @loreoliv.bsky.social and the lab turn those predictions into real data was pure magic.✨
Grateful to be part of this team!
But here I am simulating chromosomes & shuffling motifs.
Watching @loreoliv.bsky.social and the lab turn those predictions into real data was pure magic.✨
Grateful to be part of this team!
August 22, 2025 at 9:07 AM
Never thought I’d do real E. coli research, so far I used if only for cloning & protist snacks in my MSc 😅
But here I am simulating chromosomes & shuffling motifs.
Watching @loreoliv.bsky.social and the lab turn those predictions into real data was pure magic.✨
Grateful to be part of this team!
But here I am simulating chromosomes & shuffling motifs.
Watching @loreoliv.bsky.social and the lab turn those predictions into real data was pure magic.✨
Grateful to be part of this team!
Reposted by Stephan Köstlbacher
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
July 7, 2025 at 8:21 AM
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Stephan Köstlbacher
📢 New preprint alert!
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...
The Genetic Basis of Bacterial Adaptation to Hosts
Microbes colonize and interact with diverse multicellular hosts using specialized genes, many of which remain unidentified. Better understanding of host-associated gene functions is a key aspect of mi...
www.biorxiv.org
July 21, 2025 at 6:40 AM
📢 New preprint alert!
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...
Reposted by Stephan Köstlbacher
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
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
July 20, 2025 at 4:58 PM
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
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
Reposted by Stephan Köstlbacher
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
www.biorxiv.org
July 20, 2025 at 1:04 PM
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
Reposted by Stephan Köstlbacher
Exciting new research! Matthias Horn & Lukas Helmlinger from #CeMESS uncover how chlamydiae thrive in social amoebae by skipping their extracellular stage.
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
New Paper: Chlamydiae give up extracellular stage to thrive in social amoebae
Many intracellular bacteria rely on an extracellular stage to move between hosts – but what happens when that’s no longer needed? A new study, now published in Current Biology, reveals a striking exam...
cemess.univie.ac.at
July 8, 2025 at 9:58 AM
Exciting new research! Matthias Horn & Lukas Helmlinger from #CeMESS uncover how chlamydiae thrive in social amoebae by skipping their extracellular stage.
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
Reposted by Stephan Köstlbacher
Excited to share our first paper on the symbiosis between chlamydiae and social amoebae showing in detail the adaptations of endosymbionts to the social life style of their host! 🎉
Exciting new research! Matthias Horn & Lukas Helmlinger from #CeMESS uncover how chlamydiae thrive in social amoebae by skipping their extracellular stage.
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
Read their groundbreaking study in Current Biology (@currentbiology.bsky.social):
🔗 cemess.univie.ac.at/news/detail-...
New Paper: Chlamydiae give up extracellular stage to thrive in social amoebae
Many intracellular bacteria rely on an extracellular stage to move between hosts – but what happens when that’s no longer needed? A new study, now published in Current Biology, reveals a striking exam...
cemess.univie.ac.at
July 9, 2025 at 1:03 PM
Excited to share our first paper on the symbiosis between chlamydiae and social amoebae showing in detail the adaptations of endosymbionts to the social life style of their host! 🎉
Reposted by Stephan Köstlbacher
a midsummer night's dream
or
understanding chromosome organization's deep evolutionary roots
#MicroSky #Archaea #ArchaeaSky #ProtistsOnSky et al.
or
understanding chromosome organization's deep evolutionary roots
#MicroSky #Archaea #ArchaeaSky #ProtistsOnSky et al.
June 22, 2025 at 12:42 AM
a midsummer night's dream
or
understanding chromosome organization's deep evolutionary roots
#MicroSky #Archaea #ArchaeaSky #ProtistsOnSky et al.
or
understanding chromosome organization's deep evolutionary roots
#MicroSky #Archaea #ArchaeaSky #ProtistsOnSky et al.
Reposted by Stephan Köstlbacher
#NewResearch
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
www.nature.com
June 18, 2025 at 1:53 PM
#NewResearch
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
Reposted by Stephan Köstlbacher
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
April 16, 2025 at 7:14 AM
New postdoc position in our lab (2 y+): evolutionary genomics of integrons and MGEs with focus on vibrio-phage interactions. Great environment @pasteur.fr for science, career building. Super collaborators @celineloot.bsky.social @amazeld.bsky.social @fredoleroux.bsky.social 3 weeks to apply!
Reposted by Stephan Köstlbacher
Job alert ‼️
2x professorships available @uniofmanchester.bsky.social
- ecology www.jobs.manchester.ac.uk/Job/JobDetai...
- organismal biology (inc genomics, evolution etc.) www.jobs.ac.uk/job/DMI506/s...
2x professorships available @uniofmanchester.bsky.social
- ecology www.jobs.manchester.ac.uk/Job/JobDetai...
- organismal biology (inc genomics, evolution etc.) www.jobs.ac.uk/job/DMI506/s...
Senior Lecturer/Reader/Chair in Ecology:Manchester
www.jobs.manchester.ac.uk
March 26, 2025 at 5:55 AM
Job alert ‼️
2x professorships available @uniofmanchester.bsky.social
- ecology www.jobs.manchester.ac.uk/Job/JobDetai...
- organismal biology (inc genomics, evolution etc.) www.jobs.ac.uk/job/DMI506/s...
2x professorships available @uniofmanchester.bsky.social
- ecology www.jobs.manchester.ac.uk/Job/JobDetai...
- organismal biology (inc genomics, evolution etc.) www.jobs.ac.uk/job/DMI506/s...
Reposted by Stephan Köstlbacher
Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper www.cell.com/cell/fulltex... by @xujwet.bsky.social & @florianwollweber.bsky.social, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules! #TeamTomo #ArchaeaSky 1/6
March 21, 2025 at 3:16 PM
Asgard archaea have actin - but what about microtubules? Where do they come from? 🧐 Our new paper www.cell.com/cell/fulltex... by @xujwet.bsky.social & @florianwollweber.bsky.social, in collaboration with the Schleper & Wieczorek labs, describes tiny Asgard microtubules! #TeamTomo #ArchaeaSky 1/6
Reposted by Stephan Köstlbacher
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes reveals their excavate ancestry - Nature
The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemb...
www.nature.com
March 12, 2025 at 4:39 PM
🚨 New paper alert! 🚨
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
A robustly rooted tree of eukaryotes sheds light on their deep evolutionary ancestry—suggesting that the Last Eukaryotic Common Ancestor (LECA) may have had an excavate-like cell architecture. 🧵🔬 (1/) www.nature.com/articles/s41...
Reposted by Stephan Köstlbacher
Hi BlueSkyers! I'm an evolutionary biologist, microbiologist, entomologist, lover of nature, and long-time researcher on symbiosis.
I'm realizing that BlueSky is useful and generally non-toxic so here I am (having quit Facebook in Jan 2017, and Twitter in Oct 2022).
I'm realizing that BlueSky is useful and generally non-toxic so here I am (having quit Facebook in Jan 2017, and Twitter in Oct 2022).
March 11, 2025 at 9:04 PM
Hi BlueSkyers! I'm an evolutionary biologist, microbiologist, entomologist, lover of nature, and long-time researcher on symbiosis.
I'm realizing that BlueSky is useful and generally non-toxic so here I am (having quit Facebook in Jan 2017, and Twitter in Oct 2022).
I'm realizing that BlueSky is useful and generally non-toxic so here I am (having quit Facebook in Jan 2017, and Twitter in Oct 2022).
Reposted by Stephan Köstlbacher
(1/2) Preprint alert! In collaboration with @yifanzhou.bsky.social and @mkrupovic.bsky.social we describe host-parasite layers in hypersaline systems of the Danakil Depression. Haloarchaea host nanohaloarchea and both are infected by viruses (12 new families found).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 17, 2025 at 11:40 AM
(1/2) Preprint alert! In collaboration with @yifanzhou.bsky.social and @mkrupovic.bsky.social we describe host-parasite layers in hypersaline systems of the Danakil Depression. Haloarchaea host nanohaloarchea and both are infected by viruses (12 new families found).
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Stephan Köstlbacher
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea https://www.biorxiv.org/content/10.1101/2025.02.13.637844v1
February 17, 2025 at 11:35 AM
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea https://www.biorxiv.org/content/10.1101/2025.02.13.637844v1
Reposted by Stephan Köstlbacher
And now our department can also be followed pn Bluesky!! Follow us!!
February 4, 2025 at 7:23 AM
And now our department can also be followed pn Bluesky!! Follow us!!
Reposted by Stephan Köstlbacher
Congratulations to our very own John van der Oost!!!!
#BeijerinckPrize
#BeijerinckPrize
Onderzoeker en viroloog John van der Oost wint de #Beijerinck #Virologie Prijs voor zijn CRISPR-Cas onderzoek. Early career onderzoekers Carmen Embregts & Puck van Kasteren ontvangen de #BeijerinckPremie. www.knaw.nl/nieuws/voorb... @rdo-erasmusmc.bsky.social @rivm-nl.bsky.social @w-u-r.bsky.social
February 13, 2025 at 10:09 AM
Congratulations to our very own John van der Oost!!!!
#BeijerinckPrize
#BeijerinckPrize