New paper out in @cp-cellhostmicrobe.bsky.social by our super talented predoc @jonas-bio.bsky.social Congrats!

Jonas Schiller@jonas-bio.bsky.social · 2mo ago

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...

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

New in @natgenet.nature.com: a moving obituary for Peer. Francesca Ciccarelli, Jan Korbel & Christian von Mering reflect on his scientific vision, from protein domains and genome evolution to metagenomics, and on his generosity as a mentor and friend to so many. www.nature.com/articles/s41...

Peer Bork (1963–2026) - Nature Genetics

Nature Genetics - Peer Bork (1963–2026)

nature.com

Our work exploring host-microbial co-metabolism of bile acids in patients with alcohol-related liver disease (ALD) has been published in the JHEP Reports: www.sciencedirect.com/science/arti... 🪐 A big thank you to everyone involved, to the GALAXY and MicrobLiver consortia who made this possible! 🙌

Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism

Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-relat…

sciencedirect.com

🚨 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...

Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids - Nature Microbiology

Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of c...

nature.com

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 MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

cell.com

The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today: www.sciencedirect.com/science/arti...

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…

sciencedirect.com

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.

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...

cell.com

EMBL@embl.org · 6mo ago

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...

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!

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...

cell.com

Chan Yeong Kim@chanyeong-kim.bsky.social · last yr.

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

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. 🧵

EMBL@embl.org · 7mo ago

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-...

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...

Multiple protein structure alignment at scale with FoldMason

Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

science.org

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...

In remembrance of Peer Bork  | EMBL

EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

embl.org

metaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...

metaTraits: a large-scale integration of microbial phenotypic trait information

Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is

academic.oup.com

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...

Alcohol-related liver disease disrupts bile acid synthesis and is associated with compensatory gut microbiota changes

Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids...

medrxiv.org

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 🖥️🧬🦠

Chan Yeong Kim@chanyeong-kim.bsky.social · last yr.

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

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

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...

biorxiv.org

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 🧵.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.

A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1

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.

NFDI4Microbiota@nfdi4microbiota.bsky.social · last yr.

Join our next Coffee Talk on 28 April at 14:30 CEST! @podlesny.bsky.social (EMBL) presents SameStr—a new tool for strain-resolved metagenomics. Track microbes with high precision. 🔗 Zoom: ID 687 6408 9023 | PW: 826218 #Microbiome #Metagenomics #OpenScience

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/

Efficient and robust search of microbial genomes via phylogenetic compression

Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.

rdcu.be

Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder. datajournal.org/schon-wieder/

Schon wieder

Der Aufstieg der NSDAP/AfD

datajournal.org

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.

NEW ONLINE! New online! A phylogenetic approach to comparative genomics

A phylogenetic approach to comparative genomics

Nature Reviews Genetics, Published online: 08 January 2025; doi:10.1038/s41576-024-00803-0Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests.…

go.nature.com

I’m excited to share our new paper published in Nature Communications! In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups. www.nature.com/articles/s41...

A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy - Nature Communications

Here, the authors show that higher levels of the gut bacterial clade TANB77 associate with better response to cancer immunotherapy, and further demonstrate in mice that a conserved pilin from TANB77 p...

nature.com

Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses

Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...

biorxiv.org