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...

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

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...

🚨 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... ⬇️ ⬇️ ⬇️

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. 🧵

📢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

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...

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 🖥️🧬🦠

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...

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

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-...

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)

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...

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 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...

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

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

(1/5)For over a century, the hunt for new antibiotics has focused almost exclusively on bacteria and fungi. Today, that paradigm shifts. By coupling state-of-the-art AI with the vast, largely uncharted diversity of Archaea, we open a new frontier for molecular discovery.

Did you ever wonder what insights hide in the multiplets that are usually discarded in flow cytometry? 🫧 Find out in the first publication of my PhD, now out in Nature Methods! www.nature.com/articles/s41... (1/4)

At #ISMBECCB2025, @agrekova.bsky.social will present her recent work on detecting mobile genetic elements in both reference and metagenome-assembled genomes in the Microbiome track on Thursday at 3 pm. Come for a sneak peek of the content in promge.embl.de version 2 (to be released in ~1 month)!

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs

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 🖥️🧬🦠

Excited to share this @borklab.bsky.social preprint that I co-led with @chanyeong-kim.bsky.social and @podlesny.bsky.social. Thanks also to everyone else involved! #Microbiology #Metagenomics #HGT #ARG

🚨Our newest publication on the Fram Strait and #ArcticOcean is out 🚨 We explored the diversity, temporal dynamics and host-associations of Arctic #viruses over a four year time-series using long-read #metagenomics (and their global prevalence and distribution). www.nature.com/articles/s41...

Please Re-Post. Our global GRUMP microbial ocean database is out in Scientific Data! Unfractionated, single universal PCR, with Archaea, Bacteria, and Eukaryotes all on the same scale with the same denominator. Pole to pole, depths to 6000m. Lots of metadata. www.nature.com/articles/s41...

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 🧵.

1/ Ever wondered how to best quantify cell-cell neighbor preferences in tissues? We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨ Read more: doi.org/10.1101/2025...

Our new study in @naturecomms.bsky.social showing the recurrent assembly of microbial modules over polar day and night, based on four years of autonomous sampling in the Arctic www.nature.com/articles/s41... Fantastic teamwork by #AWI @mpimarinemicrobio.bsky.social @hhu.bsky.social & many others 🙂

Deep life is astonishing and diverse, and we have so much more to learn! So happy that this study is out. Big thanks to co-first author @bellahda.bsky.social and all the collaborators! www.science.org/doi/10.1126/... @science.org @mblscience.bsky.social @simonsfoundation.org #deeplife #microbiome