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Daan Speth

@daanspeth.bsky.social
1.8K followers 1.8K following 264 posts

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 globdb.org

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Reposted by Daan Speth
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Noah Houpt @noahhoupt.bsky.social · 22/09/2026
*PLEASE RE-POST* Applications for the trainee-focussed GRS immediately preceding this meeting are also now open! We will begin accepting applicants on *January 15th, 2027*. We will expedite our review for applicants requiring Visas, so please submit ASAP. www.grc.org/microbial-po...
grc.org
2027 Microbial Population Biology (GRS) Seminar GRC
The 2027 Gordon Research Seminar on Microbial Population Biology (GRS) will be held in Andover, New Hampshire. Apply today to reserve your spot.
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Will Ratcliff @wcratcliff.bsky.social · 15/09/2026
1/17 Submissions are now open for the 2027 Microbial Population Biology GRC! We expect this meeting to be extraordinarily oversubscribed. If you want to come, time is of the essence--apply ASAP! June 27–July 2 • Andover, NH www.grc.org/microbial-po...
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Sue Biggins @suebiggins.bsky.social · 21/09/2026
Here it is! @basicsci.fredhutch.org is searching for an associate or senior faculty member!
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
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/
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AHeise @aheise.bsky.social · 12/09/2026
#microsky #idsky #episky
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Florian Mayer @florianmayer.bsky.social · 11/09/2026
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
biorxiv.org
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...
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Daan Speth @daanspeth.bsky.social · 04/09/2026
@nmjgeerlings.bsky.social
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Reposted by Daan Speth
Richard Sever @richardsever.bsky.social · 03/09/2026
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...
openrxiv.org
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...
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Axel Visel @axelvisel.bsky.social · 31/08/2026
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
nature.com
A genomic catalog of Earth’s bacterial and archaeal symbionts - Nature Biotechnology
Symbiotic relationships of microorganisms are predicted and cataloged with a machine learning tool.
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Mary Munson @marymunson4.bsky.social · 26/08/2026
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/).
umassmed.edu
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...
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Mark Hibbins, Great Lakes Swashbuckler @rejectresubmit.bsky.social · 10/08/2026
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
Hibbins Lab
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Glen Dsouza @nonresidentdesi.bsky.social · 10/08/2026
📣 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
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Pilhofer Lab 🦠❄️🔬 @pilhoferlab.bsky.social · 06/08/2026
Come join us at ETH!
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Noah Whiteman @nkwhiteman.bsky.social · 06/08/2026
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
aprecruit.berkeley.edu
Assistant Professor -Genetics, Genomics, Evolution, and Development - Molecular and Cell Biology
University of California, Berkeley is hiring. Apply now!
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Marnix Medema @marnixmedema.bsky.social · 04/08/2026
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!
wur.nl
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...
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Harmit Singh Malik @harmitmalik.bsky.social · 06/08/2026
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.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 28/07/2026
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...
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Joanna Masel @joannamasel.bsky.social · 27/07/2026
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
academic.oup.com
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models
Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig
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Daan Speth @daanspeth.bsky.social · 22/07/2026
I didn’t actually check anything beyond the data availability statement yet, where it says raw data NCBI, mags on zenodo. It’d be great if they’re already at ENA :)
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Daan Speth @daanspeth.bsky.social · 22/07/2026
Congrats on the study! Since i started maintaining the.GlobDB I tend to quickly scroll to see the data availability statement on any big catalog i see. Are the MAGs not on NCBI?
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Steven Robbins @stevenjrobbins.bsky.social · 22/07/2026
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...
nature.com
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...
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Rob Edwards @linsalrob.bsky.social · 22/07/2026
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
A computer generated 3D reconstruction of a phage, based solely on its genome sequence. For this image, we started with the genome, and used PholdAPhage to create the structures. Colours are based on pLDDT scores.
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Osterman Ilya @ostermanilya.bsky.social · 13/07/2026
🚨 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...
embl.wd103.myworkdayjobs.com
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...
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Glen Dsouza @nonresidentdesi.bsky.social · 12/07/2026
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!
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Britt Koskella @bkoskella.bsky.social · 09/07/2026
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...
call.wiko-berlin.de
Wiko Application Platform
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Sebastian S. Cocioba @atinygreencell.bsky.social · 08/07/2026
@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...
biorxiv.org
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...
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Pedro Beltrao @pedrobeltrao.bsky.social · 06/07/2026
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...
nature.com
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
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A. Murat Eren (Meren) @merenbey.bsky.social · 04/07/2026
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...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 04/07/2026
Synteny-aware microbial pangenome graphs reveal blueprints of genomic variation www.biorxiv.org/content/10.64898/20…
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ssolo.bsky.social @ssolo.bsky.social · 04/07/2026
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...
biorxiv.org
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...
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erzbergerlab.bsky.social @erzbergerlab.bsky.social · 02/07/2026
Membrane protein solubilization and structure determination using de novo–designed proteins | Science www.science.org/doi/10.1126/...
science.org
Membrane protein solubilization and structure determination using de novo–designed proteins
Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a gener...
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Michael Sieber @michaelsieber.bsky.social · 01/07/2026
Have ideas for your own, independent research program in Theoretical Biology? Then come and join us as a Group Leader at the @mpi-evolbio.bsky.social in Plön, Germany!
mpg.de
Group Leader in Theoretical Biology (m/f/d)
Experience in Theoretical Biology, Applied Mathematics, Theoretical Physics
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Melanie Blokesch @mblokesch.bsky.social · 29/03/2026
Open postdoc position in my lab on HGT and interbacterial competition. We seek candidates with a PhD in microbiology (or related fields)+ strong 1st-author publications. Curious, highly motivated, and dedicated team players ready to contribute fully are encouraged to apply. Details: tiny.cc/cz01101
tiny.cc
Open Positions
-
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Daan Speth @daanspeth.bsky.social · 26/06/2026
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 🦠🖥️🧬
globdb.org
home | GlobDB
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Daan Speth @daanspeth.bsky.social · 26/06/2026
This release includes the backbone of the GlobDB, but we will release additional data in the coming months. Stay tuned!
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Daan Speth @daanspeth.bsky.social · 26/06/2026
2) The minimal quality thresholds have been upgraded to the same quality threshold that the GTDB uses (completeness - 5* contamination > 50), but using checkM2 quality scores. We opted for this change because the quality of the source datasets is less uniform as the number increases.
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Daan Speth @daanspeth.bsky.social · 26/06/2026
The taxonomy is thus not transferable between release 226 and 232, but we will strive to keep this more consistent in future releases, as the GlobDB matures.
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Daan Speth @daanspeth.bsky.social · 26/06/2026
1) Dereplication of the datasets is now done using Galah (github.com/wwood/galah), which takes into account checkM2 quality scores. This means a lot of species representative genomes have changed relative to release 226.
github.com
GitHub - wwood/galah: More scalable dereplication for metagenome assembled genomes
More scalable dereplication for metagenome assembled genomes - wwood/galah
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Daan Speth @daanspeth.bsky.social · 26/06/2026
Beyond the increased number of datasets and genomes that are included, there are two major changes in this release of the GlobDB:
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Daan Speth @daanspeth.bsky.social · 26/06/2026
@aroneys.bsky.social and @benjwoodcroft.bsky.social generated the full 7-level taxonomy, and a singleM metapackage and two sylph databases are available for profiling metagenome datasets using the GlobDB.
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Daan Speth @daanspeth.bsky.social · 26/06/2026
As with previous versions, all genome IDs are standardized and anvio contigs databases, contig nucleotide fasta, protein fasta and basic annotations (KEGG/COG/PFam/CAZymes) are available.
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Daan Speth @daanspeth.bsky.social · 26/06/2026
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 🦠🖥️🧬
globdb.org
home | GlobDB
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Brandon S. Cooper @brandonscooper.bsky.social · 18/06/2026
The lab has several new papers out led by fantastic postdocs, with important contributions from other lab members and collaborators. Each paper focuses on different aspects of Wolbachia spread and effects on hosts. The first paper was led by Dylan Shropshire and is now in Genetics.
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Elder Taylor @taylornewc.bsky.social · 18/06/2026
If Waffle House doesn’t make this their new slogan, then capitalism has failed
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Dutchscientist (the real one) @dutchscientist.bsky.social · 16/06/2026
Just to up this #microsky #microbiomesky #IDsky deadline extended until 1st of July 2026. Come and join us a a (senior) lecturer in microbiome sciences, an academic position in a collegiate school with great facilities and opportunities!
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Debnath Ghosal @debnathghosal.bsky.social · 12/06/2026
New paper alert!! We just discovered a new filament system that is widespread exclusively within CPR bacteria! www.biorxiv.org/content/10.6.... Short thread below. 🦠🔬🚀
biorxiv.org
A Novel Pilus System in Candidate Phyla Radiation Bacteria
The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15–50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primar...
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Pedro Leão @pedroleao.bsky.social · 05/06/2026
I'm happy to share the first pre-print of out Lab! 🎉 Introducing ArchaeaHQ www.biorxiv.org/content/10.6... We curated 21,644 genomes across all 4 archaeal kingdoms to bridge the gap in public datasets for computational biology What is inside ArchaeaHQ... (1/2)
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Evgenii Protasov @evgenii-protasov.bsky.social · 07/06/2026
Sulfoquinovose degradation by cow rumen microbiota #microbiology #microbiota #rumen #MicroSky @isme-microbes.bsky.social doi.org/10.1093/isme...
doi.org
Sulfoquinovose degradation by cow rumen microbiota
Abstract. Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organi
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