Jonas Schiller
@jonas-bio.bsky.social
👨🔬 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)
💻🧬 Using data science to analyze big bio-data.
🇪🇺 Part of the @embltrec.bsky.social expedition and interested in 🦠 (metaG)
Pinned
Jonas Schiller
@jonas-bio.bsky.social
· Oct 15
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
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...
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...
Reposted by Jonas Schiller
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
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
October 31, 2025 at 3:16 PM
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
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Jonas Schiller
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...
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
October 15, 2025 at 1:23 PM
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...
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
October 15, 2025 at 12:05 PM
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...
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...
Reposted by Jonas Schiller
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...
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...
www.biorxiv.org
October 14, 2025 at 6:08 AM
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...
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...
Reposted by Jonas Schiller
Variations in the latitudinal diversity gradients of the ocean microbiome www.biorxiv.org/content/10.1... #jcampubs 🌊
October 14, 2025 at 3:32 PM
Variations in the latitudinal diversity gradients of the ocean microbiome www.biorxiv.org/content/10.1... #jcampubs 🌊
Reposted by Jonas Schiller
📢 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
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
September 1, 2025 at 9:07 AM
📢 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
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
Reposted by Jonas Schiller
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...
www.biorxiv.org
August 16, 2025 at 6:34 AM
Metalog - a database of harmonised and manually curated metadata for >100,000 metagenomic samples - www.biorxiv.org/content/10.1...
Reposted by Jonas Schiller
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
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
August 15, 2025 at 1:54 PM
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
Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:
www.biorxiv.org/content/10.1...
#microsky #microbiome
Reposted by Jonas Schiller
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...
www.biorxiv.org
August 15, 2025 at 8:07 AM
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
Reposted by Jonas Schiller
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
#microsky
Metalog
Metalog is a repository of manually annotated metadata (or contextual data) for metagenomic sequencing data from across the globe.
metalog.embl.de
August 15, 2025 at 8:07 AM
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
#microsky
Reposted by Jonas Schiller
(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.
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 ...
www.nature.com
August 12, 2025 at 11:11 AM
(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.
Reposted by Jonas Schiller
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)
August 7, 2025 at 8:48 PM
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)
Reposted by Jonas Schiller
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
promge.embl.de
July 22, 2025 at 7:08 AM
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)!
Reposted by Jonas Schiller
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs
July 21, 2025 at 4:45 PM
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs
Reposted by Jonas Schiller
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 🖥️🧬🦠
#MicroSky 🖥️🧬🦠
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
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...
www.biorxiv.org
July 21, 2025 at 1:57 PM
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 🖥️🧬🦠
#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
#Microbiology #Metagenomics #HGT #ARG
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
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...
www.biorxiv.org
July 21, 2025 at 12:01 PM
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
#Microbiology #Metagenomics #HGT #ARG
Reposted by Jonas Schiller
🚨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...
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...
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...
www.nature.com
July 12, 2025 at 6:34 AM
🚨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...
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...
Reposted by Jonas Schiller
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...
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
www.nature.com
July 2, 2025 at 4:19 PM
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...
Reposted by Jonas Schiller
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 🧵.
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 🧵.
A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1
June 27, 2025 at 8:10 PM
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 🧵.
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 🧵.
Reposted by Jonas Schiller
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...
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...
April 15, 2025 at 3:50 PM
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...
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...
Reposted by Jonas Schiller
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 🙂
Fantastic teamwork by #AWI @mpimarinemicrobio.bsky.social @hhu.bsky.social & many others 🙂
February 4, 2025 at 5:02 PM
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 🙂
Fantastic teamwork by #AWI @mpimarinemicrobio.bsky.social @hhu.bsky.social & many others 🙂
Reposted by Jonas Schiller
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
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
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.
www.science.org
December 18, 2024 at 11:12 PM
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
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