Jonas Schiller

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...

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...

I am deeply grateful for Peer's mentorship on this project and throughout my PhD, and I will strive to pursue research in his spirit.

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...

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...

🚨 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-...

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.

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/...

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...

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...

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

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
🖥️🧬🦠

Save the Whales. But Save the Microbes, Too.

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

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

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

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

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)

This study was co-led by @jonas-biosky.social (@borklab.bsky.social @embl.org) and Dominic Eriksson (@ethz.ch). Big thanks to all co-authors, especially Peer Bork and our collaborators, particularly Meike Vogt, Nicolas Gruber and Shinichi Sunagawa (ETH Zürich). (6/6)

Forward looking, the improved understanding of the mechanisms behind LDGs can inform predictions of diversity under climate change scenarios, which might have distinct impacts on the diversity of different microbial lineages. (5/6)

LDG variation reflects lineage-specific strategies: Alphaproteobacteria & Cyanobacteriia diversity peak in oligotrophic gyres (nutrient-poor), consistent with their adaptations to low nutrients. Gammaproteobacteria peak outside the gyres, aligning with preferences for copiotrophic conditions. (4/6)

LDGs of the surface mixed layer are not uniform: The overall LDG was dominated by species of Cyanobacteriia and Alphaproteobacteria. Other taxonomic groups exhibit a variety of other LDG patterns. (3/6)

For the surface ocean, our models suggest higher diversity in winter than in summer. For European latitudes, our results indicate an average 57% richness increase in December, compared to June. We checked coastal time-series studies and found a similar December-June richness difference (54%). (2/6)

We found that the ocean mesopelagic layer (200-1,000 m depth) is one of the rare exceptions where LDGs are absent for marine prokaryotes. (1/6)

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...

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...

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: 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...

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