Daan Speth
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daanspeth.bsky.social
Daan Speth
@daanspeth.bsky.social
1.6K followers 1.7K following 210 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 https://globdb.org
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daanspeth.bsky.social
Daan Speth @daanspeth.bsky.social · Nov 21
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
🖥️🧬🦠
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
Reposted by Daan Speth
stevensalzberg.bsky.social
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
Reposted by Daan Speth
carlyziter.bsky.social
Love this from @stephenbheard.bsky.social on how to prioritize learning and useful discussion over tearing apart papers, and look forward to using some of these question prompts in future lab meetings: scientistseessquirrel.wordpress.com/2026/01/13/h...
How to lead a journal club you won’t be embarrassed by later
One of the jobs facing an early-career scientist, and a developing writer, is to learn what their field’s literature looks like. One of the best tools to that end is the journal club. If you’ve nev…
scientistseessquirrel.wordpress.com
January 16, 2026 at 12:01 PM
Reposted by Daan Speth
proteinmechanic.bsky.social
An interesting way to look at encoded structural characters to build alignments and trees downstream. This takes structural phylogenetics one step further in the post-AlphaFold era.

#Evolution #Science #StrPhy

On Confidence Assessment in Structure-Aware Alignments

doi.org/10.1093/gbe/...
Structome-AlignViewer: On Confidence Assessment in Structure-Aware Alignments
Abstract. Protein structure-based comparison provides a framework for uncovering deep evolutionary relationships that can escape conventional sequence-base
doi.org
January 14, 2026 at 11:07 AM
Reposted by Daan Speth
vivekmutalik.bsky.social
This is 😮

Structural insights into the assembly and evolution of a complex bacterial flagellar motor

#microsky

www.nature.com/articles/s41...
Structural insights into the assembly and evolution of a complex bacterial flagellar motor - Nature Microbiology
Structural, genetic, functional and biochemical analyses of the complex flagellar motor of Campylobacter jejuni reveal structural adaptations with an ancient origin also found more widely across bacte...
www.nature.com
January 16, 2026 at 6:22 AM
Reposted by Daan Speth
jencwaters.bsky.social
PIs & Group Leaders, do your trainees need to learn light microscopy and image analysis? Send them to us! Financial aid is available! Applications due Friday 1/30. meetings.cshl.edu/courses.aspx...
Quantitative Imaging: From Acquisition to Analysis
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
meetings.cshl.edu
January 14, 2026 at 4:20 PM
Reposted by Daan Speth
retropz.bsky.social
They also use medical illustrators to create accurate graphics

I keep a bit of a list:
scidraw.io - high-quality graphics for free download and use (all images under CC-BY licensing)
bioicons.com - free science illustrations
healthicons.org - simple icons covering a range of health contexts
Health icons
Free, open source health icons. Use in your next commercial or personal project. Editing is ok. Republishing is ok. No need to give credit.
healthicons.org
January 13, 2026 at 11:53 AM
Reposted by Daan Speth
clauswilke.com
Bioart, courtesy of the NIH. All images are in the public domain and available for download as high-quality SVGs.
bioart.niaid.nih.gov
December 17, 2024 at 1:15 AM
Reposted by Daan Speth
metalichen.bsky.social
⚡️Fully funded #PhD position in my lab at Stockholm University / SciLifeLab! If you’re interested in #lichens, #symbiosis, fungal biology, or meta-omics, please apply. Deadline Feb 1. Read more here: su.varbi.com/en/what:job/...
Black field with a macro image of a bright orange lichen Xanthoria in one of the corner. Little diagrams showing a structure of a lichen thallus with different layers in grey and green, a phylogenetic tree, and an alphafold generated structure of a protein. White text says "PhD position in Stockholm University / SciLifeLab. Lichen Biology, Symbiosis, Microbial Ecology & Evolution,Meta-omics Fully funded for 4 years. Start Apr-Sep 2026. Deadline for application: Feb 1st."
January 12, 2026 at 2:15 PM
Reposted by Daan Speth
ceesdekker.bsky.social
Latest #CDlab paper on nanopore protein sequencing now published in JACS: pubs.acs.org/doi/full/10....

Here, Justas Ritmejeris, Xiuqi Chen, collaborator Bauke Albada, and me developed a conjugation chemistry strategy for nanopore sequencing of natural peptides!
January 9, 2026 at 8:53 AM
Reposted by Daan Speth
rodrisanchez95.bsky.social
Two fantastic papers published back-to-back in @natmicrobiol.nature.com show that strictly lytic phages can persist intracellularly for long periods of time. Very much in line with ideas we had suggested in a recent study. Highly recommended reads 👇
www.nature.com/articles/s41...
January 9, 2026 at 9:50 AM
Reposted by Daan Speth
scientificdiscovery.dev
The cost of sequencing a human genome has fallen over 100,000 fold in nominal terms since 2001.

In a new visualization, I've added some of the key advances in sequencing during that timeline:
Line chart showing the dramatic decline in the cost of sequencing a human genome from 2001 to 2022, plotted on a logarithmic dollar scale. The vertical axis shows cost per genome in U.S. dollars, ranging from over $100 million down to about $500, and the horizontal axis shows year. Costs start near $100 million in 2001 during the Human Genome Project, fall gradually to around $10 million by 2005, then drop sharply after 2007 with the introduction of next-generation sequencing technologies. By 2011 costs fall below $10,000, reach around $1,000 by 2017, and continue decreasing to a few hundred dollars by the early 2020s. Annotations mark major technological milestones such as Illumina short-read sequencing, Ion Torrent semiconductor sequencing, PacBio real-time sequencing, Oxford Nanopore’s MinION, and completion of an end-to-end human genome map.
January 8, 2026 at 8:16 AM
Reposted by Daan Speth
patschloss.bsky.social
New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods.

www.biorxiv.org/content/10.6...
Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort
Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...
www.biorxiv.org
January 7, 2026 at 6:58 PM
Reposted by Daan Speth
jgi.doe.gov
Congrats to the 14 researchers with proposals accepted for our 2026 Large Scale call! These projects accelerate bioenergy innovation through genomic discovery across diverse organisms and ecosystems. 🖥️🧬🦠🌱🧪🍄

More: jgi.doe.gov/user-science...

@berkeleylab.lbl.gov @axelvisel.bsky.social
JGI Announces FY26 Large Scale Portfolio for Our Community Science Program | Joint Genome Institute
jgi.doe.gov
January 6, 2026 at 8:53 PM
Reposted by Daan Speth
cbassa.bsky.social
Happy new year! My all sky camera imaged the sky every 15 seconds and this picture shows what happened in the sky in 2025. It shows the length of the night and day with the hourglass shape, the monthly lunar cycle with the diagonal bands, the elevation of the Sun at local noon, and lots of clouds.
The image shows the hourglass shape of the length of the day and night over the 365 days in 2025. Diagonal bands indicate when the Moon was up in the night sky.
January 1, 2026 at 8:54 PM
Reposted by Daan Speth
chofski.bsky.social
If you are looking to integrate your latest genetic creation into the genome of your favourite bug, you might find our latest review now out in OUP Synthetic Biology useful. 🧬⚒️ Work led by Riesa Rohmat with input from Thea Irvine and Shivang Joshi. #genome #synbio doi.org/10.1093/synb...
January 6, 2026 at 10:58 AM
Reposted by Daan Speth
relenski.bsky.social
"The changing roles of Escherichia coli" -- a short essay by yours truly.

rdcu.be/eVtXT
The changing roles of Escherichia coli
Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.
rdcu.be
December 19, 2025 at 1:57 PM
Reposted by Daan Speth
surtlab.bsky.social
I know many of you know Joe James (of Binning Singletons)

Joe and his family had a terrible tragedy occur on Christmas. If you can give, this is a good family to help out

gofund.me/5cbfe22fe
Donate to Honoring Sarah James Through Education, organized by Joe James
Honoring Sarah James & Supporting Her Children’s Future On Christmas, our com… Joe James needs your support for Honoring Sarah James Through Education
gofund.me
January 1, 2026 at 10:05 PM
Reposted by Daan Speth
arcadiascience.com
A free, open-access library of high-quality organism illustrations for science communication
A free, open-access library of high-quality organism illustrations for science communication
We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...
doi.org
December 29, 2025 at 6:03 PM
Reposted by Daan Speth
whysharksmatter.bsky.social
I'm reviewing abstracts for an upcoming scientific conference, helping the planning team to select which attendees get a chance to present their work.

Some are amazingly good.

Some suggest that the applicant has not ever been taught how to write an abstract.

Here are some basic tips:

🧪
December 29, 2025 at 8:26 PM
Reposted by Daan Speth
isme-microbes.bsky.social
ISME20 Abstract guidelines are now available — start preparing your abstract to be able to share your latest research with the global community of microbial ecologists at ISME20, held in New Zealand, August 2026.
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
December 29, 2025 at 10:42 AM
daanspeth.bsky.social
Useful discussion on circular contigs in metagenome assembly
stevenjrobbins.bsky.social Steven Robbins @stevenjrobbins.bsky.social · 22d
Metagenomics colleagues!

Anybody know if a good piece of software to test whether Illumina contigs are circular?

@antobeck.bsky.social?
December 28, 2025 at 11:10 AM
Reposted by Daan Speth
uk-resistant.bsky.social
SO, you want to network but don't know where to begin.

1. DON'T. Make friends instead
2. It's not about what they can do for you
3. Famous people are just people first
4. If you do have to gush, don't just say 'i love your work' , pick one thing and say why. Open ended compliments are awkward
December 27, 2025 at 9:33 AM
Reposted by Daan Speth
mrillig.bsky.social
I am interested in working with an artist on a graphic novel on soil and/ or global environmental change. The lab would have money to fund this.

Do you know of any graphic artists that would be interested?
December 28, 2025 at 9:35 AM
Reposted by Daan Speth
zaminiqbal.bsky.social
Hey folks, am looking for examples of circularised/full plasmid sequences from "unusual " bacterial species, sequenced since 2020 (as independent validation for a plasmid identification tool that was trained on refseq2020+plsdb). Any tips? #microsky
December 22, 2025 at 11:03 PM
Reposted by Daan Speth
margaretbrisbin.bsky.social
This is what I’m really here for :) These are the radiolarians we have been finding. Chock full of photosynthetic symbionts in a very interesting pattern- but no idea on the species. Doing some oxygen experiments and will sequence! #oceanography #zooplankton #christmasatsea ❤️🌊 #microsky
December 23, 2025 at 2:02 AM