Sebastian Schmidt
@tsbschm.bsky.social
Lecturer in Microbiome & Health at @apcmicrobiomeirel.bsky.social & @ucc.ie Alumnus @borklab.bsky.social Microbiome, microbial ecology & metagenomics.
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)
Planetary structure and drivers of diazotroph communities reveal key reservoirs of nitrogen-fixation potential | Lucas Ustick
I 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...
linkedin.com
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 · last wk.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
Spain played a great game by making sure that France played a shitty game. Foolproof strategy.
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...
Distinct compositional changes but shared quantitative microbiome and anti-inflammatory modulations by diet
Reported 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...
cell.com
Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...
A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA
Cellular 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...
biorxiv.org
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...
Variations in the latitudinal diversity gradients of the ocean microbiome
Eriksson 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...
cell.com
A clearer way to describe microbial habitats helps researchers compare #microbiome data. A new paper in #𝐁𝐢𝐨𝐢𝐧𝐟𝐨𝐫𝐦𝐚𝐭𝐢𝐜𝐬 introduces microntology: 148 terms and curated annotations for 305,626 #metagenomic samples. @tsbschm.bsky.social @embl.org @vishnuprasoodanan.bsky.social 📰 buff.ly/FD1SYYJ
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.
microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats
AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and
academic.oup.com
Sebastian Schmidt@tsbschm.bsky.social · 7mo agoWe 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...
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...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying 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
biorxiv.org
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
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?!?
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!
More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...
biorxiv.org
Gut bacteria form #spores, but our lab models rarely match the real thing. A new review in @cp-trendsmicrobiol.bsky.social argues for developing model organisms from human gut spore‑formers. Current models miss key genetics & biology of Bacillota species common in people. 📰 buff.ly/ZWLKobR
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.
Indeed.. here is "generate the first page of a great Nature paper that will get lots of citations. It must be very novel."
GUNC pre-processed databases are now also on zenodo thanks to @fullam.bsky.social : zenodo.org/records/1963...
GUNC Reference Database Files
GUNC Reference Database Files
zenodo.org
Sebastian Schmidt@tsbschm.bsky.social · 5mo ago@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 .
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 · 4mo agoHow 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...
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!
Bioinformaticians all over the world:
ace-gtdb.bsky.social@ace-gtdb.bsky.social · 4mo agoGTDB 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 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 - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
@fullam.bsky.social has given the SPIRE website a bit of an overhaul: improved pages, nice new options to navigate, improved search, streamlined genome, study and sample pages, tidied up Downloads page, etc. Go check it out: spire.embl.de
SPIRE
spire.embl.de
This simulation-cum-benchmark study on MAG making by @tkorem.bsky.social & team looks really interesting. Loads of plots and results to work through! www.biorxiv.org/content/10.6...
biorxiv.org
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
nature.com
Sebastian Schmidt@tsbschm.bsky.social · 9mo agoWe'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...
