Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
@ettema.bsky.social
Professor of Microbiology @ WUR 🇳🇱 | Evolutionary microbiology | Exploring the Tree of Life | Archaea aficionado | Symbiotic interactions | husband, father, cat-person, eternal house renovator, secretly a Jedi knight
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
November 3, 2025 at 1:55 PM
Nature suggests you use their "Manuscript Adviser" bot to get advice before submitting
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
I uploaded the classic Watson & Crick paper about DNA structure, and the Adviser had this to say about one of the greatest paper endings of the century:
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
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
Yesterday it was 20 years since I defended my PhD thesis!
I have struggled my way through the academic system, with times when I was about to give up due to lack of funding and support.
I am proud where I am now, and what I have achieved. Thanks to everyone who supported me and believed in me!
I have struggled my way through the academic system, with times when I was about to give up due to lack of funding and support.
I am proud where I am now, and what I have achieved. Thanks to everyone who supported me and believed in me!
November 12, 2025 at 10:51 AM
Yesterday it was 20 years since I defended my PhD thesis!
I have struggled my way through the academic system, with times when I was about to give up due to lack of funding and support.
I am proud where I am now, and what I have achieved. Thanks to everyone who supported me and believed in me!
I have struggled my way through the academic system, with times when I was about to give up due to lack of funding and support.
I am proud where I am now, and what I have achieved. Thanks to everyone who supported me and believed in me!
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Do you want to do a Masters in Evolutionary Biology? The call for applying to the MEME program is now open! MEME is a fantastic 2-year MSc between four European Universities on all areas of Evolutionary Biology. Apply and study in Sweden/France/the Netherlands/Germany/USA/Switzerland! www.evobio.eu
October 24, 2025 at 9:04 AM
Do you want to do a Masters in Evolutionary Biology? The call for applying to the MEME program is now open! MEME is a fantastic 2-year MSc between four European Universities on all areas of Evolutionary Biology. Apply and study in Sweden/France/the Netherlands/Germany/USA/Switzerland! www.evobio.eu
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Interesting how companies and the financial world is racing to spend mindboggling amounts of money to build the infrastructure to train computers. But we are leaving the infrastructure to train and educate humans crumbling. The question is who will train who?
a man in a suit is holding a jacket and a cigarette .
ALT: a man in a suit is holding a jacket and a cigarette .
media.tenor.com
October 8, 2025 at 5:15 PM
Interesting how companies and the financial world is racing to spend mindboggling amounts of money to build the infrastructure to train computers. But we are leaving the infrastructure to train and educate humans crumbling. The question is who will train who?
OK, somebody should say it: the term 'one-stop-shop' has no place in academic research. Due to their diverse and exploratory nature, there is no single solution for scientific projects - else this would be routine research. RT if you agree, or feel free to argue otherwise below.
michael scott from the office is wearing a suit and tie and making a funny face .
ALT: michael scott from the office is wearing a suit and tie and making a funny face .
media.tenor.com
October 6, 2025 at 2:38 PM
OK, somebody should say it: the term 'one-stop-shop' has no place in academic research. Due to their diverse and exploratory nature, there is no single solution for scientific projects - else this would be routine research. RT if you agree, or feel free to argue otherwise below.
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...
Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social
www.nature.com/articles/s41...
Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social
September 17, 2025 at 5:41 PM
Happy to share that our story on the bacterial archaellum was published today in @natmicrobiol.nature.com
www.nature.com/articles/s41...
Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social
www.nature.com/articles/s41...
Congrats to the authors: @sshamphavi.bsky.social @loumollat.bsky.social @mariejoest.bsky.social Najwa Taib and @sgribaldo.bsky.social
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
🧵 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 8:58 AM
🧵 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...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Saddened to learn of the passing of Moselio "Elio" Schaechter—Distinguished Professor at Tufts, SDSU and UCSD—humanist and visionary leader in the fields of microbiology and scientific communication—mentor, friend, and inspiration to me and so many others
Small Things Considered
Big Things Achieved
Small Things Considered
Big Things Achieved
August 15, 2025 at 3:12 PM
Saddened to learn of the passing of Moselio "Elio" Schaechter—Distinguished Professor at Tufts, SDSU and UCSD—humanist and visionary leader in the fields of microbiology and scientific communication—mentor, friend, and inspiration to me and so many others
Small Things Considered
Big Things Achieved
Small Things Considered
Big Things Achieved
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
📣 ELIXIR has published a position paper on the importance of #OpenData infrastructure for 🌍 European competitiveness in life sciences.
Read the news 👉 https://loom.ly/22XW72k
#ResearchInfrastructure #Science4EU
Read the news 👉 https://loom.ly/22XW72k
#ResearchInfrastructure #Science4EU
June 24, 2025 at 9:01 AM
📣 ELIXIR has published a position paper on the importance of #OpenData infrastructure for 🌍 European competitiveness in life sciences.
Read the news 👉 https://loom.ly/22XW72k
#ResearchInfrastructure #Science4EU
Read the news 👉 https://loom.ly/22XW72k
#ResearchInfrastructure #Science4EU
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
8.
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
July 20, 2025 at 1:04 PM
8.
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out!
With @kassipan.bsky.social and @danieltamarit.bsky.social
With @kassipan.bsky.social and @danieltamarit.bsky.social
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 1:16 PM
Our latest work, driven by the fabulous @stephkoe.bsky.social! WitChi takes care of compositional bias in large phylogenomic datasets! WitChi is fast, efficient and free, try it out!
With @kassipan.bsky.social and @danieltamarit.bsky.social
With @kassipan.bsky.social and @danieltamarit.bsky.social
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
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 🧵
July 16, 2025 at 9:59 PM
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 🧵
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
#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...
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...
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...
www.biorxiv.org
May 23, 2025 at 10:19 AM
#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...
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...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
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
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
May 14, 2025 at 2:07 PM
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
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
On this day, 10 years ago, my lab published the @nature.com paper reporting the discovery of the Asgard archaea (Lokiarchaeota at the time), revealing the archaeal nature of eukaryotic cells, and reshaping the Tree of Life. What a ride it has been since then... www.nature.com/articles/nat...
Complex archaea that bridge the gap between prokaryotes and eukaryotes - Nature
This study identifies a clade of archaea that is the immediate sister group of eukaryotes in phylogenetic analyses, and that also has a repertoire of proteins otherwise characteristic of eukaryotes—pr...
www.nature.com
May 14, 2025 at 1:48 PM
On this day, 10 years ago, my lab published the @nature.com paper reporting the discovery of the Asgard archaea (Lokiarchaeota at the time), revealing the archaeal nature of eukaryotic cells, and reshaping the Tree of Life. What a ride it has been since then... www.nature.com/articles/nat...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Loki’s ever the trickster, but thankfully Thor knows how to put him in his place
#ArchaeaSky #Asgard #comics #comedy
#ArchaeaSky #Asgard #comics #comedy
March 20, 2025 at 7:49 PM
Loki’s ever the trickster, but thankfully Thor knows how to put him in his place
#ArchaeaSky #Asgard #comics #comedy
#ArchaeaSky #Asgard #comics #comedy
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...
LoVis4u: a locus visualization tool for comparative genomics and coverage profiles
Abstract. Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task
academic.oup.com
February 25, 2025 at 7:27 AM
Excited to share that our paper on locus visualisation tool LoVis4u is out! Entirely driven by fantastic PhD student Artyom Egorov @egorov.bsky.social academic.oup.com/nargab/artic...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
www.biorxiv.org/content/10.1... A new collaborative paper with Anja Spang, Wen-Cong Huang, @chrisrinke.bsky.social @ettema.bsky.social @ssolo.bsky.social Zheng-Shuang Hua Maraike Probst and Lenard Szantho. We investigated the phylogenetic position and metabolic evolution of Panguiarchaeum.
Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea
The Asgard archaea are a diverse archaeal phylum that includes the host lineage from which eukaryotes evolved. Due to the importance of the Asgard archaea for our understanding of cellular evolution a...
www.biorxiv.org
February 17, 2025 at 4:59 PM
www.biorxiv.org/content/10.1... A new collaborative paper with Anja Spang, Wen-Cong Huang, @chrisrinke.bsky.social @ettema.bsky.social @ssolo.bsky.social Zheng-Shuang Hua Maraike Probst and Lenard Szantho. We investigated the phylogenetic position and metabolic evolution of Panguiarchaeum.
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
January 30, 2025 at 3:16 PM
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
In case some people have missed it, I'm re-posting a link to our paper on the Anaeramoeba-Desulfobacter symbiotic system. This is one of the papers from my lab that I'm most proud of...and a huge amount of the credit goes to @jonhultqvist.bsky.social !!! www.nature.com/articles/s41...
A unique symbiosome in an anaerobic single-celled eukaryote - Nature Communications
Symbiont-housing structures are well-studied in multicellular eukaryotes but rarely in unicellular protists. This study shows that low-oxygen-adapted Anaeramoebae have symbiosomes positioning sul...
www.nature.com
January 27, 2025 at 10:46 PM
In case some people have missed it, I'm re-posting a link to our paper on the Anaeramoeba-Desulfobacter symbiotic system. This is one of the papers from my lab that I'm most proud of...and a huge amount of the credit goes to @jonhultqvist.bsky.social !!! www.nature.com/articles/s41...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
December 21, 2024 at 8:26 PM
Delighted to share our new preprint on the cell biology and genome of Stentor pyriformis, a giant ciliate that maintains Chlorella endosymbionts in surface-associated microtubule baskets.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
With today's report outlining risks on mirror life www.science.org/doi/full/10.... many have asked:
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Confronting risks of mirror life
Broad discussion is needed to chart a path forward.
www.science.org
December 12, 2024 at 9:40 PM
With today's report outlining risks on mirror life www.science.org/doi/full/10.... many have asked:
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Could mirror life survive in the wild?
Yes. While mirror life in the wild could have some significant disadvantages (like finding food it can digest), they do not appear to be insurmountable: 🧵
Reposted by Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺
We have an opening for a 4 yr PhD interested in membrane remodelling and cryo-EM/ET of a minimal cell division machinery: edu.nl/bukan
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
December 10, 2024 at 2:53 PM
We have an opening for a 4 yr PhD interested in membrane remodelling and cryo-EM/ET of a minimal cell division machinery: edu.nl/bukan
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.