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Jonas Schiller

@jonas-bio.bsky.social
155 followers 305 following 16 posts

👨‍🔬 Predoctoral Fellow at @EMBL.org in the @borklab.bsky.social. 💻🧬 Using data science to analyze big bio-data. 🇪🇺 Part of the @embltrec.bsky.social expedition and interested in 🦠 (metaG)

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Reposted by Jonas Schiller
EMBL Events @events.embl.org · 07/09/2026
At the start of 2026, EMBL lost long-serving colleague and Interim Director General Peer Bork. Join us in commemorating Peer and his legacy at the #EMBLBorkMemorial. Submit your abstract by 10 November: s.embl.org/pbs27-01-bl
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Jonas Schiller @jonas-bio.bsky.social · 12/08/2026
Thrilled to see our article „Variations of the latitudinal diversity gradients of the ocean microbiome“ as featured content in the new issue of @cp-cellhostmicrobe.bsky.social! 🔗Read the article here: www.cell.com/cell-host-mi...
cell.com
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...
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Reposted by Jonas Schiller
Bork Group at EMBL Heidelberg @borklab.bsky.social · 29/07/2026
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. 🧵
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Cell Host & Microbe @cp-cellhostmicrobe.bsky.social · 15/06/2026
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...
cell.com
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...
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Jonas Schiller @jonas-bio.bsky.social · 10/06/2026
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...
cell.com
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...
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Reposted by Jonas Schiller
Marisa Isabell Keller @maelschermarisa.bsky.social · 01/06/2026
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! 🙌
sciencedirect.com
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…
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Reposted by Jonas Schiller
Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/06/2026
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...
nature.com
Peer Bork (1963–2026) - Nature Genetics
Nature Genetics - Peer Bork (1963–2026)
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Reposted by Jonas Schiller
Lukas Malfertheiner @lukasmalf.bsky.social · 25/02/2026
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...
cell.com
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...
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Jonas Schiller @jonas-bio.bsky.social · 10/02/2026
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
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Chan Yeong Kim @chanyeong-kim.bsky.social · 09/02/2026
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.
cell.com
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 ...
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Reposted by Jonas Schiller
Bork Group at EMBL Heidelberg @borklab.bsky.social · 09/02/2026
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!
cell.com
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 ...
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Reposted by Jonas Schiller
EMBL @embl.org · 09/02/2026
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 09/02/2026
🚨 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... ⬇️ ⬇️ ⬇️
forms.gle
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...
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Reposted by Jonas Schiller
Bork Group at EMBL Heidelberg @borklab.bsky.social · 30/01/2026
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. 🧵
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supriya khedkar @khedkarsupriya.bsky.social · 27/01/2026
📢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
bioquant.uni-heidelberg.de
Join Us | Khedkar | BioQuant
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Reposted by Jonas Schiller
EMBL @embl.org · 22/01/2026
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-...
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Journal of Cell Science @jcellsci.bsky.social · 19/01/2026
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/...
Drawing showing that planetary cell biology is a field that combines environmental sciences and cell biology. Understanding cellular function and its environmental context can be useful in explaining larger-scale systems operating at the multicellular and ecological levels. Furthermore, planetary cell biology provides key insights into how biological systems might adapt, be resilient to, and even mitigate, environmental perturbations associated with the climate crisis, such as changes in temperature, pH, pressure and other conditions.
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Reposted by Jonas Schiller
Sebastian Schmidt @tsbschm.bsky.social · 13/01/2026
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...
biorxiv.org
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...
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Reposted by Jonas Schiller
Daan Speth @daanspeth.bsky.social · 21/11/2025
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 🖥️🧬🦠
doi.org
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
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Reposted by Jonas Schiller
Jack A Gilbert @gilbertjacka.bsky.social · 17/10/2025
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...
nytimes.com
Save the Whales. But Save the Microbes, Too.
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Daniel Podlesny @podlesny.bsky.social · 02/12/2025
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
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Reposted by Jonas Schiller
Suguru Nishijima @suguru-nishijima.bsky.social · 01/12/2025
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
academic.oup.com
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
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Reposted by Jonas Schiller
Sebastian Schmidt @tsbschm.bsky.social · 31/10/2025
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-...
academic.oup.com
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
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Reposted by Jonas Schiller
Bork Group at EMBL Heidelberg @borklab.bsky.social · 15/10/2025
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)
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Jonas Schiller @jonas-bio.bsky.social · 15/10/2025
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...
doi.org
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...
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Reposted by Jonas Schiller
Taylor priest @taylorpriest.bsky.social · 14/10/2025
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...
biorxiv.org
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...
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Reposted by Jonas Schiller
Cameron Thrash @jcamthrash.bsky.social · 14/10/2025
Variations in the latitudinal diversity gradients of the ocean microbiome www.biorxiv.org/content/10.1... #jcampubs 🌊
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EMBL @embl.org · 01/09/2025
📢 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
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Taylor priest @taylorpriest.bsky.social · 16/08/2025
Metalog - a database of harmonised and manually curated metadata for >100,000 metagenomic samples - www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Reposted by Jonas Schiller
Pamela Ferretti @pamferretti.bsky.social · 15/08/2025
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
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Michael Kuhn @biocs.bsky.social · 15/08/2025
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
biorxiv.org
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...
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Michael Kuhn @biocs.bsky.social · 15/08/2025
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
metalog.embl.de
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
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César de la Fuente @delafuentelab.bsky.social · 12/08/2025
(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.
nature.com
Deep learning reveals antibiotics in the archaeal proteome - Nature Microbiology
Use of artificial intelligence to mine proteomes of archaea led to the discovery of archaeasins, antimicrobials that kill drug-resistant bacteria in laboratory and animal models, offering a promising ...
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Viktoria Flore @viktoriaflore.bsky.social · 07/08/2025
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)
nature.com
Ultra-high-scale cytometry-based cellular interaction mapping - Nature Methods
Interact-omics, a high-throughput cytometry-based framework, resolves the cellular interaction landscape.
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 22/07/2025
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)!
promge.embl.de
proMGE
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Cameron Thrash @jcamthrash.bsky.social · 21/07/2025
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 21/07/2025
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 🖥️🧬🦠
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Jonas Schiller @jonas-bio.bsky.social · 21/07/2025
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
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Taylor priest @taylorpriest.bsky.social · 12/07/2025
🚨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...
nature.com
Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations - Nature Communications
Based on bulk DNA time-series sequencing of the surface Arctic Ocean, Calayag et al. show that planktonic viruses are strongly seasonal in abundance and community composition, and are correlated stron...
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Jed Fuhrman @jedfuhrman.bsky.social · 02/07/2025
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...
nature.com
Characterizing organisms from three domains of life with universal primers from throughout the global ocean - Scientific Data
Scientific Data - Characterizing organisms from three domains of life with universal primers from throughout the global ocean
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Sebastian Schmidt @tsbschm.bsky.social · 27/06/2025
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 🧵.
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Chiara Schiller @chiaraschiller.bsky.social · 15/04/2025
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...
Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.
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Matthias Wietz @matthiaswietz.bsky.social · 04/02/2025
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 🙂
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Emil Ruff @emilruff.bsky.social · 18/12/2024
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
science.org
A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide
The microbiomes of Earth’s surface and subsurface environments are different in composition, but similar in diversity.
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