🚨 A new piece of the preterm gut microbiome puzzle just fell into place!
Bifidobacterium metabolise human milk oligosaccharides (HMOs) in early life — shaping immunity, supporting gut development, and protecting against diseases like necrotising enterocolitis (NEC).
www.nature.com/articles/s41...
MicrobeAtlas is now published in Cell. 🌐🌎🦠
Explore the paper and resource to see what large-scale microbiome data reveal about global ecological patterns:
www.cell.com/cell/fulltex...
For a concrete application, see our recent work on “Community conservatism”:
www.nature.com/articles/s41...
The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today:
www.sciencedirect.com/science/arti...
I am pleased to share that our paper is now published in Cell!
www.cell.com/cell/fulltex...
I am deeply grateful to all co-authors for making this possible.
This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.
Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex...
See the quoted post below for a thread on the preprint!
In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠
🔗 Read more here: www.embl.org/news/science...
It has been two weeks since the unexpected death of Peer Bork, and all of us in his research group are deeply missing him. His scientific vision brought us together as a team, and we are immensely grateful for the time we spent together. 🧵
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
EMBL is deeply saddened by the passing of our Interim Director General Peer Bork, a pioneering scientist who left an indelible imprint on life science research in Europe and beyond.
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
Get in touch if you have feedback or would like to see other data on metaTraits. metaTraits is fully Open Access and FAIR and was supported by a Flex Fund from nfdi4microbiota.de @nfdi4microbiota.bsky.social within @nfdi.de. Many thanks to all co-authors! 8/8
A figure comparing gut microbiome composition across three groups: Gut infection (pre-FMT), post-FMT, and Healthy control. Stacked bar charts show a high relative abundance of aerotolerant bacteria (blue) in the infection group, which decreases drastically after FMT to match the healthy control group (dominated by anaerobes in dark grey). Box plots below quantify the mean abundance dropping from 42.8% to 11.8%.
2️⃣ sumTraits computes community-level trait summaries from taxonomic profiles (mOTUs, MetaPhlAn, etc.). Trait shifts can mirror environmental context: Here, aerotolerant microbes, abundant in rCDI, decrease after FMT, likely reflecting the restoration of low oxygen availability in the gut. 7/8
1️⃣ porTraits predicts traits for your genomes/MAGs (currently BacDive‑AI, GenomeSPOT, Traitar, MICROPHERRET) & pulls metaTraits context for the detected taxa. Also available on the free ☁️ workflow platform CloWM.de, or via @nextflow.io github.com/grp-bork/por.... 6/8
Bring your own data! 💻 We provide two workflows for the annotation of user-submitted data. Have a look at the examples and try them out on our metaTraits website: 5/8
Most microbial diversity is uncultured. metaTraits bridges the gap by combining culture-based trait data (@bacdive.bsky.social, @bvbrc.bsky.social, JGI/GOLD/IMG) with predictions for MAGs and genomes (SPIRE, proGenomes). All trait summaries come with provenance and links to their original data. 4/8
Search 🔍 metaTraits by NCBI or GTDB taxonomy, or directly by IDs in the underlying DBs. Filter data sources to consider in your query: You can include/exclude genome-based predictions or toggle specific culture collections to strictly control the level of evidence you need. 3/8
View traits 📊 for individual microbes, or summarized at species, genus, or family level. Explore traditional culture-based traits (e.g. aerotolerance, pH, motility), alongside metrics derived from (meta)genomics (e.g. genome size, pangenome openness, generalism, population diversity). 2/8
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
Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms.
www.medrxiv.org/content/10.1...
New preprint from the lab: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" analysing 85k metagenomes across the world, e.g. looking into generalism across habitats www.biorxiv.org/content/10.1... – see the thread below for more details!
#MicroSky 🖥️🧬🦠
Our new preprint is out!
www.biorxiv.org/content/10.1...
In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide.
@podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social
The team's first preprint is out!
Led by
@vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data?
A 🧵.
The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by
Claudia Sanchis, part of her PhD thesis!
www.biorxiv.org/content/10.1...
Europe’s choice is clear.
To put science at the heart of its economy.
To become the home of scientific freedom and collaboration.
And to welcome talent from all over the world.
I’m glad to present the first elements of our Choose Europe Initiative.
→ europa.eu/!TTbWbJ
Live in 2h: Metagenomic microbial strain tracking in the cloud! I'll be doing a quick demo showing how to use the SameStr workflow on the @nfdi4microbiota.bsky.social Cloud-based Workflow Platform (CloWM) - GUI / no-install / scalable / free for scientific use.
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social:
rdcu.be/eg4OA
1/
Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder.
datajournal.org/schon-wieder/
Screenshot von Google News: Zeit Online schreibt von vermeintlichem Hitlergruß, NTV sagt Geste ähnelt, SZ von möglichem Hitlergruß, Welt spricht von römischen Gruß oder Geste von Herzen
Weitere Screenshots von Google News. ZDF spricht von fragwürdiger Geste, T-Online schreibt Mast ihre Tiere mit Geste, BR schreibt von Hitlergruß ähnlicher Geste und so weiter
Weitere Screenshots von anderen Medien im selben Ton
Weiteres Screenshots, diesmal aber mit Watson, die als einziges Medium den Hitlergruß als solchen benennen
Dass nur eine einzige Redaktion sich hier traut, zu schreiben, was jeder sehen konnte: "Musk macht Hitlergruß" – das ist so dystopisch, ihr werft uns denen zum Fraß vor.
Die deutschen Mainstream-Medien sind soweit nach links gerutscht, dass sie einen Hitlergruß nicht mehr Hitlergruß nennen.
