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
· Jun 26
home | GlobDB
globdb.org
I'm happy to announce the release of GlobDB r232! This version contains 346,233 bacterial and archaeal genomes, based on 26 datasets.
More info globdb.org 🦠🖥️🧬
More info globdb.org 🦠🖥️🧬
Reposted by Daan Speth
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures.
🌐 martin-steinegger.github.io/Fold-Spacer/
🌐 martin-steinegger.github.io/Fold-Spacer/
September 13, 2026 at 5:01 PM
Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures.
🌐 martin-steinegger.github.io/Fold-Spacer/
🌐 martin-steinegger.github.io/Fold-Spacer/
Reposted by Daan Speth
UNC Greensboro Department of Biology is hiring for three positions this year including one in microbiology!
spartantalent.uncg.edu/postings/35918
spartantalent.uncg.edu/postings/35918
Assistant Professor Microbiology
The Department of Biology at UNC Greensboro (UNCG) seeks an individual with a strong record of accomplishment in microbiology broadly defined for a tenure-track faculty position at the rank of Assista...
spartantalent.uncg.edu
September 12, 2026 at 9:42 PM
Reposted by Daan Speth
Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6...
Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social
@tbharat-lab.bsky.social
Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social
@tbharat-lab.bsky.social
The life cycle of an archaeon with multiple membranes
Many prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, onl...
www.biorxiv.org
September 11, 2026 at 8:02 AM
Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6...
Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social
@tbharat-lab.bsky.social
Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social
@tbharat-lab.bsky.social
Clonal does not mean uniform. #MicroSky Our new review explores how genetically identical bacteria adopt different cell states, and how that diversity shapes survival, cooperation, antibiotic responses and gene transfer. 🧵 doi.org/10.1146/annu...
Decoding Bistability and Drivers of Phenotypic Variation in Bacteria
In a process known as phenotypic heterogeneity or phenotypic variation, bacteria can produce distinct phenotypes within an isogenic population in response to shifting environmental conditions. Noise i...
doi.org
September 4, 2026 at 11:23 AM
Reposted by Daan Speth
You can now update bioRxiv/medRxiv preprints with funding information after the fact.
Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper.
openrxiv.org/updating-fun...
Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper.
openrxiv.org/updating-fun...
Updating funder information on preprints - openRxiv
For the past year, bioRxiv and medRxiv authors have been able to include funder information with their preprints. This can be entered in a dedicated field during the submission process, using Research...
openrxiv.org
September 3, 2026 at 9:38 PM
You can now update bioRxiv/medRxiv preprints with funding information after the fact.
Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper.
openrxiv.org/updating-fun...
Authors often omit/don't have all funding info when submitting, but funders understandably want it there. This solves the problem without requiring you to submit a whole new paper.
openrxiv.org/updating-fun...
Reposted by Daan Speth
A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨
New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more
🔓 www.nature.com/articles/s41...
@biosci.lbl.gov @berkeleylab.lbl.gov
New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more
🔓 www.nature.com/articles/s41...
@biosci.lbl.gov @berkeleylab.lbl.gov
August 31, 2026 at 4:54 PM
A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨
New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more
🔓 www.nature.com/articles/s41...
@biosci.lbl.gov @berkeleylab.lbl.gov
New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more
🔓 www.nature.com/articles/s41...
@biosci.lbl.gov @berkeleylab.lbl.gov
Reposted by Daan Speth
Structural biology postdoctoral position open in my lab--apply now!
For more information about the lab, see www.umassmed.edu/munsonlab/.
Interested candidates should apply through the University of Massachusetts Chan Medical School jobs portal (www.ummsjobs.com/job/11668/).
For more information about the lab, see www.umassmed.edu/munsonlab/.
Interested candidates should apply through the University of Massachusetts Chan Medical School jobs portal (www.ummsjobs.com/job/11668/).
Munson Lab | Home | BMB | UMass Chan Medical School
The Munson Lab researches the mechanistic basis for the regulation of spatial and temporal specificity in membrane trafficking in the Biochemistry & Molecular Biotechnology Department at UMass Chan Me...
www.umassmed.edu
August 26, 2026 at 12:13 AM
Structural biology postdoctoral position open in my lab--apply now!
For more information about the lab, see www.umassmed.edu/munsonlab/.
Interested candidates should apply through the University of Massachusetts Chan Medical School jobs portal (www.ummsjobs.com/job/11668/).
For more information about the lab, see www.umassmed.edu/munsonlab/.
Interested candidates should apply through the University of Massachusetts Chan Medical School jobs portal (www.ummsjobs.com/job/11668/).
Reposted by Daan Speth
I'm recruiting a PhD student to work on an NSF-funded project developing new models of trait evolution for phylogenetic comparative methods! Info about the lab here:
mhibbins.github.io
Applications to our grad program are due December 1. Please share!
mhibbins.github.io
Applications to our grad program are due December 1. Please share!
Hibbins Lab
mhibbins.github.io
August 10, 2026 at 9:22 PM
I'm recruiting a PhD student to work on an NSF-funded project developing new models of trait evolution for phylogenetic comparative methods! Info about the lab here:
mhibbins.github.io
Applications to our grad program are due December 1. Please share!
mhibbins.github.io
Applications to our grad program are due December 1. Please share!
Reposted by Daan Speth
📣 We’re hiring a postdoc for @hot-mes-asu.bsky.social ! 🦠🔬
We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities.
Come do fun science with us!
apply.interfolio.com/190859
We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities.
Come do fun science with us!
apply.interfolio.com/190859
August 10, 2026 at 5:50 PM
📣 We’re hiring a postdoc for @hot-mes-asu.bsky.social ! 🦠🔬
We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities.
Come do fun science with us!
apply.interfolio.com/190859
We’re looking for someone excited about microbial interactions, ecology & evolution, and using molecular genetics and microfluidics to understand microbial communities.
Come do fun science with us!
apply.interfolio.com/190859
Reposted by Daan Speth
Come join us at ETH!
My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...
Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386
The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry
www.nature.com
August 6, 2026 at 12:19 PM
Come join us at ETH!
Reposted by Daan Speth
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
aprecruit.berkeley.edu
August 6, 2026 at 6:06 PM
I’m thrilled to share that our search for a tenure-track colleague in my *truly wonderful and collegial* Genetics, Genomics, Evolution and Development Division in the MCB Department at Berkeley @berkeleymcb.bsky.social is live! Please share this broad search widely: aprecruit.berkeley.edu/JPF05481
Reposted by Daan Speth
New postdoc opportunity in our team! Topic is computational analysis of (meta)genomic data to study evolution of plant-microbiome interactions. Part of the AEGIS consortium (aegisearth.bio/en). Apply here: www.wur.nl/en/vacancy/p...
Please RT!
Please RT!
Postdoc on computational (meta)genomic analysis
Climate change is one of the greatest challenges for global food security, requiring new approaches to understand and harness the natural diversity that enables plants and their associated microbiomes...
www.wur.nl
August 4, 2026 at 6:31 AM
New postdoc opportunity in our team! Topic is computational analysis of (meta)genomic data to study evolution of plant-microbiome interactions. Part of the AEGIS consortium (aegisearth.bio/en). Apply here: www.wur.nl/en/vacancy/p...
Please RT!
Please RT!
Reposted by Daan Speth
Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.
Join @FredHutch.org's Basic Sciences Division as an Assistant or Associate Professor and help shape the future of fundamental biology. We welcome applicants whose work will complement, extend, or bring new directions to the division.
Apply - Interfolio
apply.interfolio.com
August 6, 2026 at 3:02 AM
Come be our colleague. I have been in this Division for 27 years (4 as a postdoc and 23 as a PI). It is an amazing place to work, collaborate, and be inspired. If you are applying to be an Assistant or Associate Professor this Fall, don't miss this deadline.
Reposted by Daan Speth
Join us at Institute of Biology Leiden (IBL) as an Assistant/Associate/Full Professor in Mechanisms of Disease
Apply before 31st August, 2026:
careers.universiteitleiden.nl/job/Assistan...
Apply before 31st August, 2026:
careers.universiteitleiden.nl/job/Assistan...
July 28, 2026 at 4:00 PM
Join us at Institute of Biology Leiden (IBL) as an Assistant/Associate/Full Professor in Mechanisms of Disease
Apply before 31st August, 2026:
careers.universiteitleiden.nl/job/Assistan...
Apply before 31st August, 2026:
careers.universiteitleiden.nl/job/Assistan...
Reposted by Daan Speth
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
July 27, 2026 at 5:19 PM
Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social
Reposted by Daan Speth
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The planktonic microbiome of the Great Barrier Reef - Nature
The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...
www.nature.com
July 22, 2026 at 3:31 PM
It's out! Excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Daan Speth
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it!
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
July 22, 2026 at 1:36 AM
Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it!
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time
Reposted by Daan Speth
🚨 We're hiring! My new lab at EMBL Hamburg is looking for a Research Technician. I'm looking for someone excited by phages, metabolism, enzymes, structural biology and bacterial immunity—if you know the right person, please share this post!🧵⬇️
Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Research Technician (Osterman Group – Metabolism-driven immunity)
EMBL Hamburg / CSSB The European Molecular Biology Laboratory (EMBL) is Europe’s flagship life sciences organization, with more than 110 independent research groups across Heidelberg, Hamburg, Grenobl...
embl.wd103.myworkdayjobs.com
July 13, 2026 at 5:16 AM
🚨 We're hiring! My new lab at EMBL Hamburg is looking for a Research Technician. I'm looking for someone excited by phages, metabolism, enzymes, structural biology and bacterial immunity—if you know the right person, please share this post!🧵⬇️
Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Apply here: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Reposted by Daan Speth
Excited to share that I've been awarded a 5-year NIH MIRA (R35) from the National Institute of General Medical Sciences!
The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology.
Please share!
The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology.
Please share!
July 12, 2026 at 6:09 PM
Excited to share that I've been awarded a 5-year NIH MIRA (R35) from the National Institute of General Medical Sciences!
The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology.
Please share!
The lab is growing! We're recruiting postdocs and research techs interested in microbial ecology, quantitative microscopy, microfluidics, and molecular biology.
Please share!
Reposted by Daan Speth
Postdocs and early career folks - this is a truly wonderful opportunity to spend time in Berlin, gain time to think, and expand your network! call.wiko-berlin.de/procedure/65...
Wiko Application Platform
call.wiko-berlin.de
July 9, 2026 at 7:41 AM
Postdocs and early career folks - this is a truly wonderful opportunity to spend time in Berlin, gain time to think, and expand your network! call.wiko-berlin.de/procedure/65...
Reposted by Daan Speth
@breakliquid.bsky.social and I are delighted to say our OpenEVO preprint is finally live! An open source hand-made turbidostat that's modular, affordable, and made to be customized. Designed with love for the research community. Enjoy!!!💚
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
OpenEvo: An Open-Source Platform for Automated Evolution and Analysis
Here we introduce OpenEvo, a fully open-source, low-cost turbidostat platform for automated continuous culture and directed evolution experiments. Existing tools are expensive, complex, or lack open-s...
www.biorxiv.org
July 8, 2026 at 2:03 PM
@breakliquid.bsky.social and I are delighted to say our OpenEVO preprint is finally live! An open source hand-made turbidostat that's modular, affordable, and made to be customized. Designed with love for the research community. Enjoy!!!💚
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Daan Speth
My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...
Professor of Molecular Cell Biology and Biochemistry - Zurich, Switzerland job with ETH Zurich | 12861386
The Department of Biology at ETH Zurich invites applications for the above-mentioned tenured professorship at the Institute of Biochemistry
www.nature.com
July 6, 2026 at 7:37 AM
My department @eth-dbiol.bsky.social at ETH Zurich is hiring for a tenured professor in mol cell bio and biochemistry (associate/full). The position is within the Institute of Biochemistry (www.bc.biol.ethz.ch) and it is fairly open within their scope of research. www.nature.com/naturecareer...
Reposted by Daan Speth
New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that.
See the pre-print here:
doi.org/10.64898/202...
See the pre-print here:
doi.org/10.64898/202...
July 4, 2026 at 12:29 PM
New study by Alexander Henoch (@ahenoch.bsky.social), a PhD student in our group @hifmb.de and @awi.de, shows what it takes to bring gene synteny into microbial pangenomes, and what we learn about the variability landscape of genomes when we do that.
See the pre-print here:
doi.org/10.64898/202...
See the pre-print here:
doi.org/10.64898/202...
Reposted by Daan Speth
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation https://www.biorxiv.org/content/10.64898/2026.07.03.736256v1
July 4, 2026 at 3:18 AM
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation https://www.biorxiv.org/content/10.64898/2026.07.03.736256v1
Reposted by Daan Speth
Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Models trained with noisy genomes extend bacterial phenotype prediction into deep time
Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...
www.biorxiv.org
July 4, 2026 at 6:33 AM
Ancestral genome reconstructions get noisier the deeper in time you go. The usual response: distrust them and joke about reading entrails. Ours is to train on the noise! The result is calibrated phenotype prediction back to the LBCA deep in the Archaean. New preprint
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...