Sebastian Schmidt

Sebastian Schmidt

@tsbschm.bsky.social

Lecturer in Microbiome & Health at @apcmicrobiomeirel.bsky.social & @ucc.ie Alumnus @borklab.bsky.social Microbiome, microbial ecology & metagenomics.

664 followers641 following200 posts

Sebastian Schmidt reposted

Anne Applebaum
@anneapplebaum.wsocial.eu

"The amount of fuel Russia could export is too small, the impact on pricing too slight, the narrative too late to shape electoral outcomes: This looks, instead, like something very different: an abrupt, Hail Mary attempt to force Ukraine to surrender" www.theatlantic.com/idea/2026/10...

theatlantic.comTrump’s Message to Ukraine Is Now Crystal ClearThe president’s actions over the past 72 hours look like an effort to force Kyiv to surrender.

Sebastian Schmidt reposted

Matt Olm
@mattolm.bsky.social

My final postdoc project is out today in Nature! We show microbes co-migrated with humans out of Africa; three independent methods agree, and timing matches archaeological / genetic evidence (Fig. 4c). Seeing Fig. 4c for 1st time was one of my most memorable "eureka" moments! doi.org/10.1038/s415...

doi.orgPrehistoric global migration of vanishing gut microbes with humans - NatureMicrobial species disappearing from industrialized populations have evolved with humans over millennia and migrated worldwide with them—this may have consequences for human health.

Sebastian Schmidt reposted

bigdatabiology.bsky.social
@bigdatabiology.bsky.social

SemiBin 2.5.0 is out 🎉 concatenate_fasta() can now preserve full FASTA headers (e.g. circularity flags) when merging samples /ht Jim Downie (github.com/prototaxites) for the suggestion Agents make releases easy now: expect more frequent ones in the future github.com/BigDataBiolo...

github.comGitHub - BigDataBiology/SemiBin: SemiBin: metagenomics binning with self-supervised deep learningSemiBin: metagenomics binning with self-supervised deep learning - BigDataBiology/SemiBin
Sebastian Schmidt
@tsbschm.bsky.social

On Sep 11 2001 I was on a school trip: one week in the Netherlands, by the beach close to The Hague. That day was orienteering day: our teachers drove us out to some heather, “here’s a map and compass, see you tonight then.” So off we went: bunch of 10th graders in the middle of nowhere.

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Sebastian Schmidt
@tsbschm.bsky.social

We won the orienteering challenge that day. We were the first of just two teams that made it back on their own. Everyone else, not being idiots like us, called in to be picked up as soon as they had network again…

Sebastian Schmidt
@tsbschm.bsky.social

That day I learned a lot about the other kids in my year. Some grasped what was happening and we had sincere talks with our teachers. Others were making light of it, joking, or couldn’t be bothered to see what it was to them. Also, I’ve never been on an orienteering trip since.

Sebastian Schmidt
@tsbschm.bsky.social

On Sep 11 2001 I was on a school trip: one week in the Netherlands, by the beach close to The Hague. That day was orienteering day: our teachers drove us out to some heather, “here’s a map and compass, see you tonight then.” So off we went: bunch of 10th graders in the middle of nowhere.

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Sebastian Schmidt
@tsbschm.bsky.social

We arrived back at our bungalow camp in the afternoon. Our teachers and a bunch of other students were at the TV, shocked. I had never seen my German teacher crying. I remember stepping into the living room to a live feed from Manhattan. A minute or two later, the second tower collapsed.

Sebastian Schmidt
@tsbschm.bsky.social

We all stayed up that night and watched TV coverage until 5am or so. No one really grasped what was going on. Some kids with elder brothers were crying because they were sure their brothers were going to be immediately drafted and die in the coming war.

Sebastian Schmidt
@tsbschm.bsky.social

On Sep 11 2001 I was on a school trip: one week in the Netherlands, by the beach close to The Hague. That day was orienteering day: our teachers drove us out to some heather, “here’s a map and compass, see you tonight then.” So off we went: bunch of 10th graders in the middle of nowhere.

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Sebastian Schmidt
@tsbschm.bsky.social

Finally, we stumbled back into the reach of some antenna. The rich kids‘ phones started buzzing: sms and missed calls from their parents, from other groups, etc. We finally learned that something horrible had indeed happened in the US.

Sebastian Schmidt
@tsbschm.bsky.social

Yet we were still in the middle of nowhere. But suddenly, everyone wanted to get back with a lot more urgency. Also, it seemed a lot more desirable now to be as far away from those fighter planes as possible.

Sebastian Schmidt
@tsbschm.bsky.social

On Sep 11 2001 I was on a school trip: one week in the Netherlands, by the beach close to The Hague. That day was orienteering day: our teachers drove us out to some heather, “here’s a map and compass, see you tonight then.” So off we went: bunch of 10th graders in the middle of nowhere.

View full thread
Sebastian Schmidt
@tsbschm.bsky.social

Soon after, we noticed low flying fighter planes passing overhead, again and again. Hm, did we accidentally wander into some military training ground? This was The Hague after all: loads of NATO HQs and stuff around here, or maybe some random president visiting the NL?

Sebastian Schmidt
@tsbschm.bsky.social

This was 2001. So there was no mobile internet. We were also in a different country, so the few lucky rich kids among us who had mobile phones had switched off roaming for calls etc. And anyhow, this was 2001, so there wasn’t any signal anywhere anyway.

Sebastian Schmidt
@tsbschm.bsky.social

On Sep 11 2001 I was on a school trip: one week in the Netherlands, by the beach close to The Hague. That day was orienteering day: our teachers drove us out to some heather, “here’s a map and compass, see you tonight then.” So off we went: bunch of 10th graders in the middle of nowhere.

Sebastian Schmidt
@tsbschm.bsky.social

A few hours in, we started getting SMS from other teams: “War in the US, Manhattan is all rubble, we are all going to die.” Sure, we thought. They’re trying to scare us because we’re out here all on our own. And continued to trod through shrubbery and dune grasses.

Sebastian Schmidt reposted

Bork Group at EMBL Heidelberg
@borklab.bsky.social

Replying to @borklab.bsky.social

Led by Lucas Ustick, who has a longer write-up here: www.linkedin.com/posts/lucas-... Preprint: www.biorxiv.org/content/10.6... (5/5)

linkedin.comPlanetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential | Lucas UstickI am very excited to share our preprint on NFixPlanet, a resource and planet wide analysis of diazotrophy. Releasing this preprint feels bittersweet, as it is my first manuscript since Peer’s passing...

Sebastian Schmidt reposted

Bork Group at EMBL Heidelberg
@borklab.bsky.social

New preprint from the lab! "Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential" Nitrogen fixation is scattered right across the prokaryotic tree — but it's heterotrophs, not cyanobacteria, that dominate the potential. 🧵

bioRxiv Microbiology@biorxiv-microbiol.bsky.social

Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential https://www.biorxiv.org/content/10.64898/2026.07.27.741065v1

Sebastian Schmidt reposted

W. Florian Fricke
@wffricke.bsky.social

Is it not just “good” and “bad” bacteria but their absolute abundance, i.e, quantitative microbiome parameters (QMPs) that control the #microbiome’s effect on the host? Check out our new paper in @cp-cellreports.bsky.social: www.cell.com/cell-reports...

cell.comDistinct compositional changes but shared quantitative microbiome and anti-inflammatory modulations by dietReported gut microbiome associations with diet and disease are frequently inconsistent between studies and interventions. Ruple et al. show that a high-fiber diet and time-restricted feeding induce si...

Sebastian Schmidt reposted

Masaru Nobu
@masarunobu.bsky.social

Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...

biorxiv.orgA representative of a ubiquitous bacterial lineage parasitically feeds on host RNACellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of red...

Sebastian Schmidt reposted

Jonas Schiller
@jonas-bio.bsky.social

Our new paper „Variations in the latitudinal diversity gradients of the ocean microbiome“ was just published in @cp-cellhostmicrobe.bsky.social 🥳 We present a global analysis of prokaryotic #biodiversity in the surface and mesopelagic layers of the ocean 🦠🌊 www.cell.com/cell-host-mi...

cell.comVariations in the latitudinal diversity gradients of the ocean microbiomeEriksson et al. conduct a global marine microbiome diversity analysis and demonstrate how the surface ocean latitudinal diversity gradient is disproportionately shaped by a few species-rich taxa. Mask...
Sebastian Schmidt
@tsbschm.bsky.social

Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com : academic.oup.com/bioinformati... Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social ! See the thread below for more details.

academic.oup.commicrontology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitatsAbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and
Sebastian Schmidt@tsbschm.bsky.social

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...

biorxiv.orgmicrontology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitatsSummary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...

Sebastian Schmidt reposted

bigdatabiology.bsky.social
@bigdatabiology.bsky.social

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

biorxiv.orgThe elusive resistome: a global comparison reveals large discrepancies among detection pipelinesIdentifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174

Sebastian Schmidt reposted

Nature Microbiology
@natmicrobiol.nature.com

Our May issue with a focus on technological advances in microbiology is out now! Read about 🌱defence evasion by plant pathogens 🦠E. coli capsule revival 💻multiomic microbiome integration 🐁chronic chikungunya infection 🦀 bacteria in cancer immunotherapy and much more: shorturl.at/Wtzkp #MicroSky

Sebastian Schmidt reposted

Dr. Holly Walters
@manigarm.bsky.social

I'm sorry, what? In writing my first monograph, I spent six weeks trying to track down a citation in TWO languages I didn't know. And good thing too, because the citation was wrong. That's scholarship. That's research. You know, the thing we're trained to do?!?

Sebastian Schmidt reposted

Joerg Lau
@joerglau.bsky.social

Hostage taker to hostages: This is your hostage crisis, too. Don’t just sit there waiting for me to negotiate, stand up and do something to get us all out of here!

Sebastian Schmidt reposted

Jonathan Eisen
@phylogenomics.bsky.social

Reposting this from April 1, 2007 in honor of Craig Venter. I did this as an April Fool's joke - sharing it as a PDF. I got stressed when I found out Craig had seen it and knew it was by me. But he loved it and said it was OK to share it more widely. So then I posted it on the web.

Sebastian Schmidt reposted

Theo Sanderson
@theo.io

Replying to @pedrobeltrao.bsky.social

Indeed.. here is "generate the first page of a great Nature paper that will get lots of citations. It must be very novel."

Sebastian Schmidt
@tsbschm.bsky.social

GUNC pre-processed databases are now also on zenodo thanks to @fullam.bsky.social : zenodo.org/records/1963...

zenodo.orgGUNC Reference Database FilesGUNC Reference Database Files
Sebastian Schmidt@tsbschm.bsky.social

@fullam.bsky.social has pushed a new #GUNC release, v1.1.0: github.com/grp-bork/gun... It fixes some bugs, updates some underlying databases and brings new features (e.g. you can now BYODB – bring your own database). GUNC v1.1.0 is also live on #bioconda .

github.comRelease v1.1.0 · grp-bork/guncSummary ^^^^^^^ This release adds support for two new reference databases (ProGenomes 3, GTDB r214) and a custom database option. A new gunc check subcommand validates your environment before submi...
Sebastian Schmidt
@tsbschm.bsky.social

This is bad. Personally, I maintain that if a study does not release data, it should be considered not on the scientific record and can therefore be ignored. To restrict, you need very strong (exceptional) reasons. Predictably, that's not a popular stance with many though.

A. Murat Eren (Meren)@merenbey.bsky.social

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

merenlab.orgUnfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism StudyThe myth of open data, reproducibility, responsibility, and accountability in science, and your role in it

Sebastian Schmidt reposted

Bork Group at EMBL Heidelberg
@borklab.bsky.social

Due to some IT problems, the Bork group homepage and various services such as SPIRE and Metalog are unfortunately going to be unavailable for a couple of days. We're sorry for that and hope that the outage can soon be resolved!

Sebastian Schmidt
@tsbschm.bsky.social

Bioinformaticians all over the world:

ace-gtdb.bsky.social@ace-gtdb.bsky.social

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

gtdb.ecogenomic.orgGTDB - Genome Taxonomy DatabaseThe Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

Sebastian Schmidt reposted

ace-gtdb.bsky.social
@ace-gtdb.bsky.social

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

gtdb.ecogenomic.orgGTDB - Genome Taxonomy DatabaseThe Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
Sebastian Schmidt
@tsbschm.bsky.social

It’s also encouraging to see that much of this aligns with our pipeline updates for the next version of SPIRE which we vibe-benchmarked based on much less sophisticated tests and setups.