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
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
A free, open-access library of high-quality organism illustrations for science communication
Reposted by Daan Speth
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:
🧪
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
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:
🧪
Some are amazingly good.
Some suggest that the applicant has not ever been taught how to write an abstract.
Here are some basic tips:
🧪
Reposted by Daan Speth
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
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
December 29, 2025 at 10:42 AM
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
Learn more: isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Useful discussion on circular contigs in metagenome assembly
Metagenomics colleagues!
Anybody know if a good piece of software to test whether Illumina contigs are circular?
@antobeck.bsky.social?
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
Useful discussion on circular contigs in metagenome assembly
Reposted by Daan Speth
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
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
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
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
Reposted by Daan Speth
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?
Do you know of any graphic artists that would be interested?
December 28, 2025 at 9:35 AM
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?
Do you know of any graphic artists that would be interested?
Reposted by Daan Speth
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
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
Reposted by Daan Speth
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
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
Reposted by Daan Speth
As the year ends, we decided to select our favorite papers of 2025
Turns out, it is impossible as we love them all!
So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology.
Here is a glimpse into #EditorPicks of 2025
#MicroSky 🦠
Turns out, it is impossible as we love them all!
So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology.
Here is a glimpse into #EditorPicks of 2025
#MicroSky 🦠
December 19, 2025 at 3:03 PM
As the year ends, we decided to select our favorite papers of 2025
Turns out, it is impossible as we love them all!
So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology.
Here is a glimpse into #EditorPicks of 2025
#MicroSky 🦠
Turns out, it is impossible as we love them all!
So, we picked 'some' that exhibit the range of microbiology highlighted through the columns of Nature Microbiology.
Here is a glimpse into #EditorPicks of 2025
#MicroSky 🦠
Reposted by Daan Speth
Late job posting: My department is hiring a tenure-track faculty member in microbiology! Please share with anyone interested in working at a PUI. We have a preference for someone who can teach Medical Microbiology, but other than that the focus is open-ended. Happy to answer qs.
Microbiologist (AA27034)
All Job Postings will close at 12:01 a.m. CT on the specified Closing Date (if designated). Working Title: Microbiologist (AA27034) Institution: Minnesota State University, Mankato Classification Titl...
minnstate.wd1.myworkdayjobs.com
December 19, 2025 at 9:28 PM
Late job posting: My department is hiring a tenure-track faculty member in microbiology! Please share with anyone interested in working at a PUI. We have a preference for someone who can teach Medical Microbiology, but other than that the focus is open-ended. Happy to answer qs.
Reposted by Daan Speth
A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2
Isolation of Crenothrix bacteria reveals the distinct ecophysiologies of filamentous methanotrophs and adaptations to redox stress
At the dawn of modern microbiology, Cohn observed abundant filamentous bacteria in drinking water wells that he named Crenothrix polyspora. Subsequent research has revealed the methanotrophic metaboli...
doi.org
December 19, 2025 at 10:21 AM
A quick microbio present before the holidays 🎁 >150 years after their first description, filamentous "Crenothrix bacteria" are now in stable laboratory culture! In our pre-print, we probe the unique physiology & ecology of the "lacustrine" group of these enigmatic methane-oxidizing microbes... 1/2
Reposted by Daan Speth
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Reposted by Daan Speth
DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form!
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
Tell Us Your JGI Portal Stories
The JGI Portal teams (IMG, Mycocosm, Phycocosm, Phytozome, and SMC) would love to sit with you (over Zoom) to hear your stories relating to your usage of the portals, your unsupported use cases, and p...
jointgeno.me
December 15, 2025 at 5:16 PM
DOE's Office of Science is making a big push into AI, and that includes our work at the @jgi.doe.gov . We want to hear your thoughts (+ and -) on AI-enabled biological data. Consider joining one of our interviews or focus groups by filling out this form!
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
🧪🧬🦠🖥️ #secmet
jointgeno.me/PortalStorie...
Reposted by Daan Speth
AITHYRA Global Adjunct Principal Investigator Program:
Advancing AI-Driven Life Science Through Global Collaborations
Learn more about the Program: aithyra.at/fileadmin/do...
Application Deadline, 30 January 2026: application@aithyra.at
#AITHYRA #GlobalAdjunctPI
Advancing AI-Driven Life Science Through Global Collaborations
Learn more about the Program: aithyra.at/fileadmin/do...
Application Deadline, 30 January 2026: application@aithyra.at
#AITHYRA #GlobalAdjunctPI
December 15, 2025 at 3:12 PM
AITHYRA Global Adjunct Principal Investigator Program:
Advancing AI-Driven Life Science Through Global Collaborations
Learn more about the Program: aithyra.at/fileadmin/do...
Application Deadline, 30 January 2026: application@aithyra.at
#AITHYRA #GlobalAdjunctPI
Advancing AI-Driven Life Science Through Global Collaborations
Learn more about the Program: aithyra.at/fileadmin/do...
Application Deadline, 30 January 2026: application@aithyra.at
#AITHYRA #GlobalAdjunctPI
Reposted by Daan Speth
“Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota” by @kohtzarchaeota.bsky.social, Sylvia Nupp, and myself is out in Science Advances. 90% enriched culture of a methyl-dismutating thermoproteotal methanogen. #Microsky 🧪 tinyurl.com/bdcc3uzs
Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota
The cultivation of a group of methanogens illuminates their metabolic diversity and the evolution of archaea.
www.science.org
December 12, 2025 at 7:22 PM
“Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota” by @kohtzarchaeota.bsky.social, Sylvia Nupp, and myself is out in Science Advances. 90% enriched culture of a methyl-dismutating thermoproteotal methanogen. #Microsky 🧪 tinyurl.com/bdcc3uzs
Aha, I realized that I forgot to add #ProtistsOnSky and #SymbioSky to this thread highlighting our recent respiratory endosymbiont paper.
Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬
Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!
doi.org/10.1093/isme...
Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations!
doi.org/10.1093/isme...
Validate User
doi.org
December 12, 2025 at 12:15 PM
Aha, I realized that I forgot to add #ProtistsOnSky and #SymbioSky to this thread highlighting our recent respiratory endosymbiont paper.
Really happy to see this paper from @mpimarinemicrobio.bsky.social urea use by ammonia oxidizing archaea in the ocean out.
The work was led by talented PhD student Jördis Stührenberg and @kathikitzinger.bsky.social, now assistant prof (and colleague again) at @cemess.bsky.social.
The work was led by talented PhD student Jördis Stührenberg and @kathikitzinger.bsky.social, now assistant prof (and colleague again) at @cemess.bsky.social.
🧪🦠🌊
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Urea use drives niche separation between dominant marine ammonia oxidizing archaea - Nature Communications
Two groups of ammonia-oxidizing archaea drive marine nitrification. Stuehrenberg et al. reveal that their distribution reflects substrate use, with one relying on urea and the other on ammonia to main...
www.nature.com
December 11, 2025 at 12:01 PM
Really happy to see this paper from @mpimarinemicrobio.bsky.social urea use by ammonia oxidizing archaea in the ocean out.
The work was led by talented PhD student Jördis Stührenberg and @kathikitzinger.bsky.social, now assistant prof (and colleague again) at @cemess.bsky.social.
The work was led by talented PhD student Jördis Stührenberg and @kathikitzinger.bsky.social, now assistant prof (and colleague again) at @cemess.bsky.social.
Reposted by Daan Speth
🧪🦠🌊
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Urea use drives niche separation between dominant marine ammonia oxidizing archaea - Nature Communications
Two groups of ammonia-oxidizing archaea drive marine nitrification. Stuehrenberg et al. reveal that their distribution reflects substrate use, with one relying on urea and the other on ammonia to main...
www.nature.com
December 11, 2025 at 11:02 AM
🧪🦠🌊
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Curious on #niche differentiation of marine #AOA #Nitrosopumilus and #Nitrosopelagicus?
#Urea is (part of) the answer!
Very happy this fun study led by
@mpimarinemicrobio.bsky.social is out:
shorturl.at/wajjh
Big shout out to Joerdis and Hannah for pushing this over the finish line!
Reposted by Daan Speth
New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species.
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
December 10, 2025 at 12:43 PM
New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species.
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Daan Speth
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
December 9, 2025 at 1:58 PM
I'm teaching Statistical Rethinking again starting Jan 2026. This time with live lectures, divided into Beginner and Experienced sections. Will be a lot more work for me, but I hope much better for students.
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
I will record lectures & all will be found at this link: github.com/rmcelreath/s...
Reposted by Daan Speth
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
Reposted by Daan Speth
🎄🧬 It’s December – time for an 'Immunocalendar': “CRISPR CRISPR KNÄUSCHEN”!
Every day we open a new door onto a different prokaryotic immune system, with extra love for archaeal hosts.
Crafted by the Zink Group within our department :)
Have a wonderful Christmas time! ✨
Every day we open a new door onto a different prokaryotic immune system, with extra love for archaeal hosts.
Crafted by the Zink Group within our department :)
Have a wonderful Christmas time! ✨
December 7, 2025 at 12:25 PM
🎄🧬 It’s December – time for an 'Immunocalendar': “CRISPR CRISPR KNÄUSCHEN”!
Every day we open a new door onto a different prokaryotic immune system, with extra love for archaeal hosts.
Crafted by the Zink Group within our department :)
Have a wonderful Christmas time! ✨
Every day we open a new door onto a different prokaryotic immune system, with extra love for archaeal hosts.
Crafted by the Zink Group within our department :)
Have a wonderful Christmas time! ✨
Reposted by Daan Speth
Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh
December 8, 2025 at 3:04 PM
Phages are full of genes of unknown function that are likely adaptive in specific conditions.
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh
New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out
tinyurl.com/bdcfrejh
Reposted by Daan Speth
Paid internship opportunity for Master’s students in the Netherlands 🇳🇱
If you’re studying computer science, bioinformatics or molecular biology, this could be the perfect springboard for you.
A collaboration with the Embassy of the Kingdom of the Netherlands.
www.ebi.ac.uk/about/jobs/i...
If you’re studying computer science, bioinformatics or molecular biology, this could be the perfect springboard for you.
A collaboration with the Embassy of the Kingdom of the Netherlands.
www.ebi.ac.uk/about/jobs/i...
December 8, 2025 at 12:04 PM
Paid internship opportunity for Master’s students in the Netherlands 🇳🇱
If you’re studying computer science, bioinformatics or molecular biology, this could be the perfect springboard for you.
A collaboration with the Embassy of the Kingdom of the Netherlands.
www.ebi.ac.uk/about/jobs/i...
If you’re studying computer science, bioinformatics or molecular biology, this could be the perfect springboard for you.
A collaboration with the Embassy of the Kingdom of the Netherlands.
www.ebi.ac.uk/about/jobs/i...
Reposted by Daan Speth
Does bioinformatics have an abandonware problem? My thoughts after reflecting on the Tucson Genomic Standards Consortium Meeting for a while: rbartelme.github.io/blog/the-aba... #bioinformatics #computationalbiology #FAIRdata #HPC #datascience
Bioinformatics Code Rot: Do We Have an Abandonware Problem?
Graduate students need novel tools to publish. Labs lack funding for maintenance. How can we build sustainable bioinformatics software without fixing the incentive structure?
rbartelme.github.io
December 5, 2025 at 5:25 PM
Does bioinformatics have an abandonware problem? My thoughts after reflecting on the Tucson Genomic Standards Consortium Meeting for a while: rbartelme.github.io/blog/the-aba... #bioinformatics #computationalbiology #FAIRdata #HPC #datascience