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

Ocean microbial latitudinal diversity gradients Ocean microbial LDG is depth dependent w/surface LDG shaped by a few species-rich taxa. Taxonomic resolution unmasks patterns, revealing structuring of ocean microbiome & foundation for predicting change 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

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

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

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

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

Never thought I'd co-first author a paper that appears on the screens on campus, that makes me very happy😃 www.cell.com/cell/fulltex... Check out the paper and get amazing summaries from the EMBL communications team and a thread by @chanyeong-kim.bsky.social

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...

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...

🚨 Do you work on microbial-mediated biotransformation of chemical compounds? 🧪 We would value your input to help us develop a standardized reporting framework for Xenobiotics–Microbiome interactions! 👉 Take the short survey (6–8 min): forms.gle/JNATejDrV2LR... ⬇️ ⬇️ ⬇️

MIX-MB (Minimum Information about Xenobiotics-Microbiome Biotransformation) - Community Consensus Survey

This survey aims to establish the Minimum Information about Xenobiotics-Microbiome Biotransformation (MIX-MB) reporting standards. As we move toward an era of AI-driven discovery, the structural and f...

forms.gle

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-...

📢Job opportunity📢 Two year Alliance Interinstitutional #Postdoc position in "mapping antibiotic resistance spread among human gut microbes" available in my group in collaboration with Heidelberg University Hospital www.bioquant.uni-heidelberg.de/groups/khedk... #AMR #microbiome

Health + Life Science Alliance Heidelberg Mannheim @hlsalliance.bsky.social · 7mo ago

The Alliance is looking for outstanding, international early career scientists/ clinician scientists, for bridging projects between two or more Alliance partner institutions. 👉Deadline on 3/31/26 5pm CEST Info on our webpage at: www.health-life-sciences.de/opportunitie... #postdoc

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-...

Cell biology for a sustainable future – a call to action from Camila Costa, Eliott Flaum, @dhlashwayo.bsky.social, Marie Jacobovitz, Guillermina Kubaczka, Samuel Lovat, Eliya Milshtein, @hannaszafranska.bsky.social and @sorayazwahlen.bsky.social. journals.biologists.com/jcs/article/...

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...

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats

Summary. 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...

biorxiv.org

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 🖥️🧬🦠

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

Microbes sustain all ecosystems yet they’re nearly absent from conservation frameworks. The @IUCN Microbial Conservation Specialist Group aims to change that. Honored to co-chair this global effort. Great @nytimes piece by Carl Zimmer: www.nytimes.com/2025/10/17/s...

Save the Whales. But Save the Microbes, Too.

nytimes.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

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

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

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

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

Our newest preprint is the work of two talented PhD students: Dominic Eriksson (working in the labs of Meike Vogt, Nicolas Gruber & Shinichi Sunagawa @ethz.ch) and @jonas-bio.bsky.social from our group @embl.org, investigating latitudinal diversity gradients of the ocean microbiome (🧵 linked below)

Jonas Schiller@jonas-bio.bsky.social · 10mo ago

Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear. In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses. doi.org/10.1101/2025...

Latitudinal diversity gradients (LDGs) are found across 🌱🐨🦠 but their underlying mechanisms remain unclear. In this study, we highlight that LDGs are not universal in marine microbiomes but reflect lineage-specific ecological strategies and environmental responses. doi.org/10.1101/2025...

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...

doi.org

Interested in how microbial #diversity is structured across the global #oceans? Check out our newest preprint! We show that latitudinal diversity gradients are taxon-specific, reflecting differing ecological strategies and their responses to environmental gradients www.biorxiv.org/content/10.1...

Variations in the latitudinal diversity gradients of the ocean microbiome

Latitudinal diversity gradients (LDGs), typically declining from the equator to the poles, are among the most pervasive macroecological patterns, yet their generality and underlying drivers in the oce...

biorxiv.org

Variations in the latitudinal diversity gradients of the ocean microbiome www.biorxiv.org/content/10.1... #jcampubs 🌊

📢 Recruitment for the EMBL International PhD Programme is officially open! At EMBL, we train young scientists to become skilled and creative future leaders in academia and other sectors. Join us and get a head start on your career in life sciences! bit.ly/47mmiFF

Metalog - a database of harmonised and manually curated metadata for >100,000 metagenomic samples - www.biorxiv.org/content/10.1...

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

biorxiv.org

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠 Proud to have contributed to Metalog, the latest @borklab.bsky.social resource: www.biorxiv.org/content/10.1... #microsky #microbiome

We hope many of you will find it useful, and will continue to add data. Here's the preprint: www.biorxiv.org/content/10.1... - hopefully coming soon to a NAR Database Issue near you 😅 Thanks to everyone in the @borklab.bsky.social @embl.org who contributed to this! 7/7

Metalog: curated and harmonised contextual data for global metagenomics samples

Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals and the environment. While sequencing data is deposited in public databases, the associated context...

biorxiv.org

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky