Bork Group at EMBL Heidelberg

Scientific Community Manager EMBL is Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation with more than 110 independent research groups and teams performing scientific research in disci...

The Data Science team at EMBL is hiring for two open positions! First, for a Scientific Community Manager, focusing on community aspects and training on data science. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Had a great time yesterday presenting my efforts to use large-scale computational analyses to better understand marine microbes and their impact on carbon cycling. Thanks #SAME18 for the opportunity!

Our scientific organisers opened ‘The human microbiome’ symposium by giving us a brief update on their most recent work 🦠 #EESMicrobiome

🔹Mani Arumugam, University of Copenhagen
🔹Ami Bhatt, Stanford University School of Medicine
🔹Peer Bork, EMBL Heidelberg
🔹Nicola Segata, University of Trento

New preprint from lab: www.biorxiv.org/content/10.1... describing the Metalog database of manually annotated contextual data for >110k metagenomics samples around the globe metalog.embl.de

See the thread below from @biocs.bsky.social for more info!

We’re looking for curious, innovative science leaders at EMBL Heidelberg! 🔬🧬🦠

Join a vibrant, interdisciplinary community where collaboration and innovation are nurtured at all levels.

Take a look at these four open positions 👇

Group Leader – Molecular Systems Biology Unit Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

Postdoctoral position in human gut microbiome and bioinformatics - VIB About the Lab Thelab of JeroenRaes(VIB, KU Leuven) is home to a vibrant, dynamic and international group of researchers in the field of gut microbial ecology and its

We're hiring a postdoc!🚨

Study human-associated microbial communities in health & disease.

🔬Requirements:
- PhD in bioinformatics, microbiology, or related field
- Expertise in omics data analysis
- Micro & molecular bio techniques are a plus!

Apply now!🌟
jobs.vib.be/j/119682/pos...

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)!

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...

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

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 🖥️🧬🦠

Environmental Technician or Engineer (Soil Lead) The European Molecular Biology Laboratory (EMBL) is Europe’s flagship research institution for the life sciences, bringing together over 110 independent research groups and service teams across six si...

TREC is hiring! @embl.org is looking for a field technician/engineer to coordinate soil sampling: plan activities, apply protocols, lead site scouting, coordinate teams & more. Join an amazing international team exploring a hidden universe beneath our feet. Please spread the word! bit.ly/4eSTPbZ

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa.
🔗 microbiomejournal.biomedcentral.com/articles/10....

It's finally out!🎉

We known that the #microbiome confers colonization resistance against #pathogens, we know that some meds 💊 affect gut microbes 🦠

So, do 💊 alter colonization resistance? It turns out that some do! If you wanna know more, check out our latest work 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 🧵.

After a long silence on X (for obvious reasons), the Zeller Lab is now on Bluesky! We’ll post updates soon on what’s been happening in the lab over the past few months. For the future, we promise to share our News in a more timely manner here on this channel.
#Microbiome #Bioinformatics #ZellerLab

📥 You have only until 24 June to submit your abstract for 'The human microbiome'❗

🔬💊 Explore cutting-edge breakthroughs in #microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. Join #EESMicrobiome 🦠🔍

➡️ https://s.embl.org/ees25-08-bl

EESMicrobiome

Join us at #EESMicrobiome!

Organisers Mani Arumugam (#uni_copenhagen), Ami Bhatt (@stanfordpress.bsky.social), Peer Bork (@borklab.bsky.social) and Nicola Segata (#CIBIO_UniTrento) look forward to welcoming #microbiome scientists in September at @embl.org!

@events.embl.org

In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex Cryo-electron tomography has emerged as powerful technology for in-cell structural biology, and in combination with breakthroughs in protein structure prediction, offers a unique opportunity for illum...

This is just an excellent preprint by Rasmus Jensen and colleagues from Julia Mahamid's lab @embl.org - a tour de force of Cryogenic electron tomography to do in cell structural biology in which they discover a new complex and solve its structure and function! www.biorxiv.org/content/10.1...

Open postdoc position in my lab @earlhaminst.bsky.social @quadraminstitute.bsky.social
We will generate large-scale soil metagenomes to research the impact of agriculture on healthy soil microbiomes, developing strategies to increase carbon retention: jobs.earlham.ac.uk/Details.asp?...
Please RT

Live in 2h: Metagenomic microbial strain tracking in the cloud! I'll be doing a quick demo showing how to use the SameStr workflow on the @nfdi4microbiota.bsky.social Cloud-based Workflow Platform (CloWM) - GUI / no-install / scalable / free for scientific use.

Building of a research institute by the sea in Roscoff, France

Two years ago, TREC began in Roscoff. Sampling at 120+ sites across Europe was supported by @embl.org custom-built mobile lab and @taraoceans-science.bsky.social schooner, enabling on-site processing across land and sea. Now this work continues, with 100s of projects initiated 📸 Kinga Lubowiecka

Zoomed out view of scientists sampling a beach on the TREC expedition

TREC is now on Bluesky! The expedition has gathered samples all along Europe’s coasts – now scientists are exploring what the data tell us. We’ll be sharing insights into this amazing ongoing work! Spread the word! @embl.org @taraoceans-science.bsky.social @embrc-eu.bsky.social 📸Massimo Del Prete

Join our next Coffee Talk on 28 April at 14:30 CEST!
@podlesny.bsky.social (EMBL) presents SameStr—a new tool for strain-resolved metagenomics. Track microbes with high precision.
🔗 Zoom: ID 687 6408 9023 | PW: 826218
#Microbiome #Metagenomics #OpenScience

Two men standing at a table, smiling to camera.

We announce changes in EMBL leadership as Edith Heard steps down as Director General.

EMBL will be led jointly by Peer Bork as Interim Director General and Ewan Birney in a new role of Executive Director until the appointment of EMBL’s next Director General.

www.embl.org/news/embl-an...

Apparently the job application already appears closed, despite the deadline being today. Please contact us via email instead if you would like to apply!

Welcome to the Bluesky page of the Developmental Biology Unit at EMBL @embl.org! Follow us for updates on our research #devbio and activities

One week left to apply!

If you're looking for a postdoc in analyzing environmental microbiome data in beautiful Heidelberg, this is your chance!

Postdoctoral Fellow - Computational Analysis of Environmental Microbiome Data We are seeking a highly motivated computational biologist to join the research group of Peer Bork within the Molecular Systems Biology Unit as a postdoctoral fellow. This bioinformatics group works on...

We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
In the past two years, @embl.org scientists have gathered more than 3000 soil, sediment & water samples from Europe's coastlines within the #TREC expedition (1/2)

We are looking for PhD students!

Fully funded studentships available to work on a range of topics, from small proteins to developing computational tools to study the global microbiome

Welcome to Dr. Askarbek Orakov, a postdoc, who recently joined the Hutlab and Dr. Seth Rakoff-Nahoum's lab at Boston Children's. They will be working on the female genital tract virome and pediatric bone marrow transplantation microbiome. Askarbek completed his PhD at EMBL in the Bork group.