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
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
🎄🧬 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
Reposted by Daan Speth
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
GitHub - bede/deacon: Fast DNA search and [host] depletion using minimizers
Fast DNA search and [host] depletion using minimizers - bede/deacon
github.com
December 3, 2025 at 7:40 PM
github.com/bede/deacon
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
For anyone still using Bowtie2 for filtering or depletion of host sequences or specifics, I can recommend Deacon from @bedec.bsky.social . It is so much faster and easier than Bowtie2, and its performance is equal or better (tested with metagenomes and mitogenomes).🧬 & 🖥️
Reposted by Daan Speth
People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 5, 2025 at 11:03 AM
People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding
more sulfoquinovose work @loyteam.bsky.social
Cosmopolitan marine bacteria facilitate a vast phytoplankton-derived sulfonate-based carbon flow through sulfoquinovosidases www.nature.com/articles/s41... #jcampubs 🌊
December 5, 2025 at 6:44 PM
more sulfoquinovose work @loyteam.bsky.social
Reposted by Daan Speth
We are hiring! Come join #TeamBioSci and help us bring science solutions to the world @berkeleylab.lbl.gov!
The @jgi.doe.gov has an opening for a Bioinformatician to join the Synthetic Biology Group. Ian Blaby is the Hiring Manager.
jobs.lbl.gov/jobs/bioinfo...
The @jgi.doe.gov has an opening for a Bioinformatician to join the Synthetic Biology Group. Ian Blaby is the Hiring Manager.
jobs.lbl.gov/jobs/bioinfo...
December 4, 2025 at 10:13 PM
We are hiring! Come join #TeamBioSci and help us bring science solutions to the world @berkeleylab.lbl.gov!
The @jgi.doe.gov has an opening for a Bioinformatician to join the Synthetic Biology Group. Ian Blaby is the Hiring Manager.
jobs.lbl.gov/jobs/bioinfo...
The @jgi.doe.gov has an opening for a Bioinformatician to join the Synthetic Biology Group. Ian Blaby is the Hiring Manager.
jobs.lbl.gov/jobs/bioinfo...
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 5, 2025 at 4:20 PM
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...
Reposted by Daan Speth
Protist–bacteria partnerships are more common in wastewater treatment plants than we thought. In this ISME communications paper, we uncovered widespread denitrifying endosymbionts inside ciliates, their global distribution, and their temporal dynamics across WWTPs.🦠
academic.oup.com/ismecommun/a...
academic.oup.com/ismecommun/a...
Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome
Abstract. Effective wastewater treatment is of critical importance for preserving public health and protecting natural environments. Key processes in waste
academic.oup.com
December 5, 2025 at 10:49 AM
Protist–bacteria partnerships are more common in wastewater treatment plants than we thought. In this ISME communications paper, we uncovered widespread denitrifying endosymbionts inside ciliates, their global distribution, and their temporal dynamics across WWTPs.🦠
academic.oup.com/ismecommun/a...
academic.oup.com/ismecommun/a...
Reposted by Daan Speth
Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs
December 4, 2025 at 2:18 PM
Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs
Reposted by Daan Speth
Great question!
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
Dear senior profs who have written tenure letters.
Can you help demystify the process for some junior profs up for tenure soon?
What do you look for? How do you make your evaluation?
We are told that the letters are the most important part of the file, but not what letter writers look for.
1/
Can you help demystify the process for some junior profs up for tenure soon?
What do you look for? How do you make your evaluation?
We are told that the letters are the most important part of the file, but not what letter writers look for.
1/
December 4, 2025 at 9:17 PM
Great question!
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
1) First and foremost, we evaluate a candidate based on the departmental guidelines and expectations provided. We don't hold the candidate to arbitrary standards, or even to those of our own institution unless asked to do so. We assess the materials against the guidelines provided.
Reposted by Daan Speth
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 3, 2025 at 8:50 PM
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Very happy to have contributed to the data analysis resulting from this monumental sampling effort.
Big congrats to everyone involved.
Big congrats to everyone involved.
Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The Microflora Danica atlas of Danish environmental microbiomes - Nature
Microflora Danica—an atlas of Danish environmental microbiomes—reveals that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity.
www.nature.com
December 3, 2025 at 9:47 PM
Very happy to have contributed to the data analysis resulting from this monumental sampling effort.
Big congrats to everyone involved.
Big congrats to everyone involved.
Reposted by Daan Speth
We're advertising for a bacteriology technician and a post-doc to work on AI-guided antibiotic development as part of a large multidisciplinary Fleming Initiative project:
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
www.imperial.ac.uk
December 3, 2025 at 7:23 AM
We're advertising for a bacteriology technician and a post-doc to work on AI-guided antibiotic development as part of a large multidisciplinary Fleming Initiative project:
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
www.imperial.ac.uk/jobs/search-...
Reposted by Daan Speth
🔊 APPLY NOW for our #MarMic #MSc/#PhD program!
Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more.
⏳ Open until Feb 28 2026
➡ marmic.mpg.de
#graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de
Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more.
⏳ Open until Feb 28 2026
➡ marmic.mpg.de
#graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de
December 2, 2025 at 1:47 PM
🔊 APPLY NOW for our #MarMic #MSc/#PhD program!
Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more.
⏳ Open until Feb 28 2026
➡ marmic.mpg.de
#graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de
Come to #Bremen and take an interdisciplinary approach to #marine #microbiology, #molecularbiology, #biochemistry, #evolution and more.
⏳ Open until Feb 28 2026
➡ marmic.mpg.de
#graduatestudents #marinescience #sciencecareer #IMPRS @maxplanck.de
Reposted by Daan Speth
We have got an open position for a Max Planck Director in the field of Systems Biology and Bioengineering.
There is no more comfortable position.
Please nominate qualified candidates, you can also nominate yourself!
#microsky 🧪
There is no more comfortable position.
Please nominate qualified candidates, you can also nominate yourself!
#microsky 🧪
#openposition #directorposition #hiring #bioprocessengineering #biosystems #syntheticbiology #biotechnology | Max Planck Institute for Dynamics of Complex Technical Systems
𝐂𝐚𝐥𝐥 𝐟𝐨𝐫 𝐍𝐨𝐦𝐢𝐧𝐚𝐭𝐢𝐨𝐧𝐬 𝐟𝐨𝐫 𝐭𝐡𝐞 𝐏𝐨𝐬𝐢𝐭𝐢𝐨𝐧 𝐨𝐟 𝐚 𝐃𝐢𝐫𝐞𝐜𝐭𝐨𝐫 at the Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
The MPI for Dynamics of Complex Technical Systems expects...
www.linkedin.com
December 3, 2025 at 6:22 AM
We have got an open position for a Max Planck Director in the field of Systems Biology and Bioengineering.
There is no more comfortable position.
Please nominate qualified candidates, you can also nominate yourself!
#microsky 🧪
There is no more comfortable position.
Please nominate qualified candidates, you can also nominate yourself!
#microsky 🧪
Reposted by Daan Speth
GFF was originally conceived of as an interchange format for chaining together gene subfeatures (splice sites, promoters, exons, etc) predicted by various specialized tools (HMMs, decision trees, neural nets, SVMs); rather like GENSCAN, but with the idea you could mix & match subfeature predictors
December 3, 2025 at 5:41 AM
GFF was originally conceived of as an interchange format for chaining together gene subfeatures (splice sites, promoters, exons, etc) predicted by various specialized tools (HMMs, decision trees, neural nets, SVMs); rather like GENSCAN, but with the idea you could mix & match subfeature predictors
Reposted by Daan Speth
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes
Abstract. Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is st
academic.oup.com
December 3, 2025 at 2:34 AM
🦠🧪🧬🚨 New paper and database alert: the new IMG/VR release is now MetaVR ! We have a new website - meta-virome.org - with quick search capabilities for the >24M viruses, >12M vOTUs, and >42M protein clusters (including >790k with predicted structures !). academic.oup.com/nar/advance-...
Reposted by Daan Speth
💎MRC AIM PhD advert💎 Uncharted territory - the Akkermansia muciniphila import system.
Liang Wu, David Tourigny, and I are looking for someone to work on how A. muciniphila imports mucin.
www.findaphd.com/phds/project...
Liang Wu, David Tourigny, and I are looking for someone to work on how A. muciniphila imports mucin.
www.findaphd.com/phds/project...
Uncharted territory - the Akkermansia muciniphila import system at University of Birmingham on FindAPhD.com
PhD Project - Uncharted territory - the Akkermansia muciniphila import system at University of Birmingham, listed on FindAPhD.com
www.findaphd.com
December 2, 2025 at 7:08 PM
💎MRC AIM PhD advert💎 Uncharted territory - the Akkermansia muciniphila import system.
Liang Wu, David Tourigny, and I are looking for someone to work on how A. muciniphila imports mucin.
www.findaphd.com/phds/project...
Liang Wu, David Tourigny, and I are looking for someone to work on how A. muciniphila imports mucin.
www.findaphd.com/phds/project...
Reposted by Daan Speth
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
phd.pages.ista.ac.at
December 2, 2025 at 8:44 AM
📢 We have multiple open PhD positions to study bacterial immune systems using cutting-edge cryo-EM, microbiology, and biochemistry in our group! Join us and uncover how bacterial defenses eliminate predators and engineer next-gen biotech tools.
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
🔥 Apply by Jan 8, 2026
Details: phd.pages.ista.ac.at
Reposted by Daan Speth
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
November 30, 2025 at 7:51 PM
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Reposted by Daan Speth
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!
Nanoscale imaging of native symbiotic animal tissue using amultimodal large volume imaging pipeline for cryo-electrontomography https://www.biorxiv.org/content/10.1101/2025.11.30.691379v1
December 1, 2025 at 4:35 AM
CryoET of microbes inside an animal organ? Yes it’s possible! Check out our new preprint showing how we did it! What an amazing collaboration with amazing scientists who made this possible!