Sebastian Schmidt
@tsbschm.bsky.social
Lecturer in Microbiome & Health at @apcmicrobiomeirel.bsky.social & @ucc.bsky.social
Alumnus @borklab.bsky.social
Microbiome, microbial ecology & metagenomics.
Alumnus @borklab.bsky.social
Microbiome, microbial ecology & metagenomics.
Reposted by Sebastian Schmidt
Three decades of biodiversity data, published one decade after we started the project!
Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years.
www.nature.com/articles/s41...
Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years.
www.nature.com/articles/s41...
Airborne eDNA captures three decades of ecosystem biodiversity - Nature Communications
Quantifying ecosystem dynamics is critical in the face of rapid environmental change. This study uses airborne eDNA to quantify changes in organism abundances across the tree of life and reveal a regi...
www.nature.com
December 19, 2025 at 8:06 AM
Three decades of biodiversity data, published one decade after we started the project!
Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years.
www.nature.com/articles/s41...
Our new paper in @NatureComms shows how airborne eDNA from archived aerosol filters can track ecosystem changes across the tree of life—2700+ genera, weekly resolution, 34 years.
www.nature.com/articles/s41...
This is amazing.
I once sang the „original“ (Chant des Oiseaux) with an 8 voice a Capella ensemble and this is still one of my fondest choral memories!
I once sang the „original“ (Chant des Oiseaux) with an 8 voice a Capella ensemble and this is still one of my fondest choral memories!
December 18, 2025 at 10:46 PM
This is amazing.
I once sang the „original“ (Chant des Oiseaux) with an 8 voice a Capella ensemble and this is still one of my fondest choral memories!
I once sang the „original“ (Chant des Oiseaux) with an 8 voice a Capella ensemble and this is still one of my fondest choral memories!
Reposted by Sebastian Schmidt
This column captures the core of my Trump shock. It’s not about this or that policy, as awful as most of them are, or about the US abandoning Europe. It is the moral decay, the turn against basic human decency, the lack of manners that keep any good society together.
www.nytimes.com/2025/12/16/o...
www.nytimes.com/2025/12/16/o...
Opinion | Our Petty, Hollow, Squalid Ogre in Chief
www.nytimes.com
December 17, 2025 at 7:49 AM
This column captures the core of my Trump shock. It’s not about this or that policy, as awful as most of them are, or about the US abandoning Europe. It is the moral decay, the turn against basic human decency, the lack of manners that keep any good society together.
www.nytimes.com/2025/12/16/o...
www.nytimes.com/2025/12/16/o...
At this point, Europeans should insist that Russia withdraws from Donbas, Luhansk, Crimea, Belgorod, Belarus,Transnistria, Abchasia, S Ossetia, Chechnya, Dagestan, Karelia and Königsberg as a prerequisite before a cease fire can even be discussed.
❌🇺🇦🇺🇸 Zelensky did not accept Witkoff's proposal to withdraw troops from Donbas at the talks in Berlin, - AFR.
Ukrainian side insists that the ceasefire should be WITHOUT prior territorial concessions, the maximum they agree to is along the front line.
Ukrainian side insists that the ceasefire should be WITHOUT prior territorial concessions, the maximum they agree to is along the front line.
December 15, 2025 at 1:58 PM
At this point, Europeans should insist that Russia withdraws from Donbas, Luhansk, Crimea, Belgorod, Belarus,Transnistria, Abchasia, S Ossetia, Chechnya, Dagestan, Karelia and Königsberg as a prerequisite before a cease fire can even be discussed.
The Salomonic solution would be to give out bonds based on frozen Russian assets, but tie all risks of litigation directly to EU payments to Hungary and Slovakia.
If Russia comes for the money (and wins in court), just take it out of allotments to HUN and SVK until the bill is settled. Win-win-win.
If Russia comes for the money (and wins in court), just take it out of allotments to HUN and SVK until the bill is settled. Win-win-win.
December 12, 2025 at 9:04 AM
The Salomonic solution would be to give out bonds based on frozen Russian assets, but tie all risks of litigation directly to EU payments to Hungary and Slovakia.
If Russia comes for the money (and wins in court), just take it out of allotments to HUN and SVK until the bill is settled. Win-win-win.
If Russia comes for the money (and wins in court), just take it out of allotments to HUN and SVK until the bill is settled. Win-win-win.
Reposted by Sebastian Schmidt
Viruses are found in almost every ecosystem across the planet.
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
December 3, 2025 at 3:57 PM
Viruses are found in almost every ecosystem across the planet.
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Reposted by Sebastian Schmidt
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
December 2, 2025 at 5:52 PM
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Reposted by Sebastian Schmidt
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
academic.oup.com
December 1, 2025 at 4:41 AM
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
Reposted by Sebastian Schmidt
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
🖥️🧬🦠
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
November 21, 2025 at 4:21 PM
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 Sebastian Schmidt
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 2:02 PM
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes academic.oup.com/nar/advance-... #jcampubs
Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published!
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Abstract. The pervasive availability of publicly available microbial genomes has opened many new avenues for microbiology research, yet it also demands rob
academic.oup.com
November 20, 2025 at 8:50 AM
Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published!
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...
Reposted by Sebastian Schmidt
🚨Job claxon 🚨
University College Cork is looking to appoint a lecturer in Medical Microbiology into a permanent, non-clinical post
A great opportunity in a microbiology powerhouse
For details go to my.corehr.com/pls/uccrecru... and enter reference number 092153
University College Cork is looking to appoint a lecturer in Medical Microbiology into a permanent, non-clinical post
A great opportunity in a microbiology powerhouse
For details go to my.corehr.com/pls/uccrecru... and enter reference number 092153
University College Cork Vacancies
my.corehr.com
November 18, 2025 at 10:55 PM
🚨Job claxon 🚨
University College Cork is looking to appoint a lecturer in Medical Microbiology into a permanent, non-clinical post
A great opportunity in a microbiology powerhouse
For details go to my.corehr.com/pls/uccrecru... and enter reference number 092153
University College Cork is looking to appoint a lecturer in Medical Microbiology into a permanent, non-clinical post
A great opportunity in a microbiology powerhouse
For details go to my.corehr.com/pls/uccrecru... and enter reference number 092153
We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Hidden but discoverable diversity in the global microbiome
Cataloguing Earth's biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing cens...
www.biorxiv.org
November 18, 2025 at 8:53 PM
We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Tja…
"Heck of a job, Bobby."
"If the outbreaks cannot be extinguished by January, the anniversary of the first cases in Texas, the United States will lose what is known as “elimination status” as determined by the World Health Organization."
(gift link)
"If the outbreaks cannot be extinguished by January, the anniversary of the first cases in Texas, the United States will lose what is known as “elimination status” as determined by the World Health Organization."
(gift link)
C.D.C. Links Measles Outbreaks in Multiple States for the First Time
www.nytimes.com
November 18, 2025 at 1:42 PM
Tja…
Reposted by Sebastian Schmidt
Reposted by Sebastian Schmidt
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
November 13, 2025 at 10:09 AM
“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla.
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
doi.org/10.1038/s415...
@benjwoodcroft.bsky.social @rhysnewell.bsky.social
🧵1/6
Its a pretty safe bet that Donald Trump will be in the official champions photo after the World Cup 2026 final, standing in first line and holding the trophy.
You know the ending of this story, right?
FIFA president Gianni Infantino will award the first-ever FIFA Peace Prize during the 2026 World Cup draw in DC on December 5.
The prize will honour individuals who have helped unite people and promote peace.
FIFA president Gianni Infantino will award the first-ever FIFA Peace Prize during the 2026 World Cup draw in DC on December 5.
The prize will honour individuals who have helped unite people and promote peace.
November 6, 2025 at 10:07 AM
Its a pretty safe bet that Donald Trump will be in the official champions photo after the World Cup 2026 final, standing in first line and holding the trophy.
Reposted by Sebastian Schmidt
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
"As a scientist, how do you feel about the US Secretary of Health?"
October 28, 2025 at 3:25 PM
"As a scientist, how do you feel about the US Secretary of Health?"
Reposted by Sebastian Schmidt
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
ICE footage from the US is just shocking. As a German it hits particularly hard because they act like the SS and SA did in 1930s Nazi Germany.
And I have been asked countless times, "why did regular people not stand up to the Nazis". Never thought we'd one day have to ask Americans the same thing.
And I have been asked countless times, "why did regular people not stand up to the Nazis". Never thought we'd one day have to ask Americans the same thing.
October 11, 2025 at 6:44 PM
ICE footage from the US is just shocking. As a German it hits particularly hard because they act like the SS and SA did in 1930s Nazi Germany.
And I have been asked countless times, "why did regular people not stand up to the Nazis". Never thought we'd one day have to ask Americans the same thing.
And I have been asked countless times, "why did regular people not stand up to the Nazis". Never thought we'd one day have to ask Americans the same thing.