Daan Speth
@daanspeth.bsky.social
Computational microbiologist. Senior scientist at @cemess.bsky.social, @univie.ac.at.
Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology.
Maintainer of the GlobDB genome database https://globdb.org
Microbial ecology, mostly of nitrogen cycle microbes, and data driven physiology.
Maintainer of the GlobDB genome database https://globdb.org
Pinned
Daan Speth
@daanspeth.bsky.social
· Nov 21
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
doi.org
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
🖥️🧬🦠
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
🖥️🧬🦠
Reposted by Daan Speth
The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
February 12, 2026 at 12:00 PM
The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Reposted by Daan Speth
Please share!
PhD position at the University of Copenhagen. Start date: 1st of June!
The project integrates field work, RNAseq, MALDI-MSI & FISH to explore composition, regulation, and resilience of termite host-gut symbiont metabolism.
👉 employment.ku.dk/phd?show=156...
⏳ Deadline 23/2/26
PhD position at the University of Copenhagen. Start date: 1st of June!
The project integrates field work, RNAseq, MALDI-MSI & FISH to explore composition, regulation, and resilience of termite host-gut symbiont metabolism.
👉 employment.ku.dk/phd?show=156...
⏳ Deadline 23/2/26
February 11, 2026 at 7:39 PM
Please share!
PhD position at the University of Copenhagen. Start date: 1st of June!
The project integrates field work, RNAseq, MALDI-MSI & FISH to explore composition, regulation, and resilience of termite host-gut symbiont metabolism.
👉 employment.ku.dk/phd?show=156...
⏳ Deadline 23/2/26
PhD position at the University of Copenhagen. Start date: 1st of June!
The project integrates field work, RNAseq, MALDI-MSI & FISH to explore composition, regulation, and resilience of termite host-gut symbiont metabolism.
👉 employment.ku.dk/phd?show=156...
⏳ Deadline 23/2/26
Reposted by Daan Speth
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Bluesky Map
Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.
bluesky-map.theo.io
February 8, 2026 at 10:59 PM
I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
Reposted by Daan Speth
Postdoc position on Asgard archaea in Thiago’s new lab for someone well trained in biochemistry, cloning, and protein purification:
international.au.dk/about/profil...
international.au.dk/about/profil...
Postdoc in Archaea Microbiology - Vacancy at Aarhus University
Vacancy at Department of Biology - Microbiology, Aarhus University
international.au.dk
February 10, 2026 at 2:36 PM
Postdoc position on Asgard archaea in Thiago’s new lab for someone well trained in biochemistry, cloning, and protein purification:
international.au.dk/about/profil...
international.au.dk/about/profil...
Reposted by Daan Speth
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Daan Speth
Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?
Then come and join our group !
Then come and join our group !
🚨We are hiring a Bioinformatician who will be embedded in our lab and work with members of the NCCR Microbiomes at ETH Zurich, as well as the Institute of Microbiology.🚨
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
nccr-microbiomes.ch
jobs.ethz.ch/job/view/JOP...
Bioinformatician in Microbiome Research
jobs.ethz.ch
January 23, 2026 at 6:18 PM
Do you have experience in bioinformatics and are looking for a new challenge? To immerse yourself in a group and institute doing highly diverse research?
Then come and join our group !
Then come and join our group !
Reposted by Daan Speth
How does catalysis emerge from non-catalytic domains?
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
@claudele.bsky.social et al. studied the fundamental question of how enzymatic activity emerges by focusing on type B dihydrofolate reductases, suggesting DfrB domains evolved rudimentary catalysis from a binding capacity.
🔗 doi.org/10.1093/molbev/msaf215
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf215
#evobio #molbio
From Binding to Catalysis: Emergence of a Rudimentary Enzyme Conferring Intrinsic Antibiotic Resistance
Abstract. How does enzymatic activity emerge? To shed light on this fundamental question, we study type B dihydrofolate reductases (DfrB), which were disco
doi.org
October 8, 2025 at 2:32 PM
How does catalysis emerge from non-catalytic domains?
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
In our new paper, we show that catalytic activity can arise without conserved active-site residues — through multimerization and electrostatic features instead.
A striking case of catalysis evolving from binding.
Reposted by Daan Speth
New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
The Dayhoff Exchange Score: A new metric to quantify entropic site saturation in amino acid datasets prior to phylogenetic analysis
Abstract. Entropic site saturation is a persistent problem in phylogenetic analyses, where it can hinder the accuracy of topology reconstruction. It is fun
academic.oup.com
February 1, 2026 at 10:18 AM
New research published! I wanted to write about this, because I think the DE-Score *might* be the thing I'm proudest of so far!
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
All my career I have dreamt of finding something so clean. The DE-Score is a way to tell when amino acid data stops being informative. 1/7
academic.oup.com/sysbio/advan...
Reposted by Daan Speth
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Research Group Leader
Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...
embl.wd103.myworkdayjobs.com
January 30, 2026 at 9:02 AM
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
Reposted by Daan Speth
We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...
jobs.uni-jena.de/jobposting/9...
PhD student bioinformatics: Viral strategies in the global Microverse
jobs.uni-jena.de
January 29, 2026 at 12:08 PM
We have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link:
jobs.uni-jena.de/jobposting/9...
jobs.uni-jena.de/jobposting/9...
Reposted by Daan Speth
Microbiology is seeking Editors to help ensure the publication of high-quality research and to foster engagement across the microbiology community.
Expertise in biotechnology, regulation, sensing, signalling or AMR is especially welcome.
🗓️ Apply by 16 February: https://microb.io/4qKdgJ6
Expertise in biotechnology, regulation, sensing, signalling or AMR is especially welcome.
🗓️ Apply by 16 February: https://microb.io/4qKdgJ6
<i>Microbiology</i> Editors: Call for expressions of interest
microb.io
January 29, 2026 at 12:30 PM
Microbiology is seeking Editors to help ensure the publication of high-quality research and to foster engagement across the microbiology community.
Expertise in biotechnology, regulation, sensing, signalling or AMR is especially welcome.
🗓️ Apply by 16 February: https://microb.io/4qKdgJ6
Expertise in biotechnology, regulation, sensing, signalling or AMR is especially welcome.
🗓️ Apply by 16 February: https://microb.io/4qKdgJ6
🦠🖥️🧬
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:17 PM
🦠🖥️🧬
Reposted by Daan Speth
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
www.biorxiv.org
January 29, 2026 at 12:07 PM
Calling all OrthoFinder users!
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny.
GLADE runs directly on OrthoFinder results.
www.biorxiv.org/content/10.6...
github.com/lauriebelch/...
(1/10)
Reposted by Daan Speth
Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
January 28, 2026 at 8:28 PM
Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
Reposted by Daan Speth
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research
The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...
research.pasteur.fr
January 28, 2026 at 11:19 AM
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
Reposted by Daan Speth
www.wur.nl/en/vacancy/f...
Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!
Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!
Full Professor and Chair Laboratory of Biophysics
We are looking for a Full Professor in the Biophysics chair group, part of Wageningen University & Research (WUR)
www.wur.nl
January 28, 2026 at 5:20 AM
www.wur.nl/en/vacancy/f...
Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!
Become our new colleague (and next door neighbor) and lead a chair/group/department of Biophysics at Wageningen University. Reach out to me for info and please spread!!!
Reposted by Daan Speth
We have two funded postdoctoral positions available. Topics encompass:
-Next gen light-sheet fluorescence microscopy instrumentation
-Structured illumination microscopy and other approaches to extend the resolution limit.
-Nonlinear microscopy combined with adaptive optics / phase conjugation
-Next gen light-sheet fluorescence microscopy instrumentation
-Structured illumination microscopy and other approaches to extend the resolution limit.
-Nonlinear microscopy combined with adaptive optics / phase conjugation
January 27, 2026 at 10:29 PM
We have two funded postdoctoral positions available. Topics encompass:
-Next gen light-sheet fluorescence microscopy instrumentation
-Structured illumination microscopy and other approaches to extend the resolution limit.
-Nonlinear microscopy combined with adaptive optics / phase conjugation
-Next gen light-sheet fluorescence microscopy instrumentation
-Structured illumination microscopy and other approaches to extend the resolution limit.
-Nonlinear microscopy combined with adaptive optics / phase conjugation
Reposted by Daan Speth
On the importance of preprints, regardless of whether you are Team Sponge or Team Jelly:
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
What were the first animals? The fierce sponge–jelly battle that just won’t end
For almost two decades, scientists have debated whether sponges or comb jellies are the first animal lineage. Now some are calling for a more harmonious approach.
www.nature.com
January 27, 2026 at 2:38 PM
On the importance of preprints, regardless of whether you are Team Sponge or Team Jelly:
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
'King says that she wishes she had posted the study as a preprint so that the errors could have been caught sooner.'
www.nature.com/articles/d41...
Reposted by Daan Speth
Here’s my 3-step framework to learn Bioinformatics or learn anything in life 👇
January 27, 2026 at 2:45 PM
Here’s my 3-step framework to learn Bioinformatics or learn anything in life 👇
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
January 26, 2026 at 1:27 PM
With the release of anvi'o v9, the 300k+ contigs databases available for download on the GlobDB website are now compatible with both the development version and the latest stable release (v9) of anvi'o.
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
More info:
globdb.org/news
Thanks #anvio team!
🖥️🧬🦠
Reposted by Daan Speth
Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)
January 22, 2026 at 10:06 PM
Hello world! I am excited to announce my lab is open at the University of Utah in the Department of Biochemistry. We are looking for scientists at all levels interested in studying host-virus interactions in both bacteria and animals. Come join us in beautiful Utah! (photo is 10 steps from lab)
Reposted by Daan Speth
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology
Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...
www.nature.com
January 22, 2026 at 2:24 PM
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Reposted by Daan Speth
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 22, 2026 at 7:40 AM
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
Reposted by Daan Speth
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
GitHub - ebiggers/libdeflate: Heavily optimized library for DEFLATE/zlib/gzip compression and decompression
Heavily optimized library for DEFLATE/zlib/gzip compression and decompression - ebiggers/libdeflate
github.com
January 20, 2026 at 1:37 AM
🗜️⚡ If you use gzip/gunzip a lot in your pipelines, switch to the faster"libdeflate" versions instead! They use modern CPU capabilities to achieve a 2-3x speedup.
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
libdeflate is in conda, and "libdeflate-gzip" and "libdeflate-gunzip" are drop-in replacements. #unix
github.com/ebiggers/lib...
Reposted by Daan Speth
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org
Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning
Mirdita Lab builds scalable bioinformatics methods.
mirdita.org
January 20, 2026 at 11:07 AM
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
mirdita.org