We're up to 1000 studies in metalog.embl.de ! For the past year the focus was on finding inconsistencies in the data and creating the website, but now I have more time to go through the backlog of annotated issues to do QC and load them into the database.

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...

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 👇

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!

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)!

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 🖥️🧬🦠

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

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

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

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.

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

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

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...

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!

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.

Pre-registration is now open for our second (free) course on phylogenomic data analysis and visualization using ETE, funded by @cziscience.bsky.social First time to cover new ETE4 features: Interactive viz of huge tree, profiling... In Madrid, April 21-25. Travel fellowships available!

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)

If you would like to gain practical experience in how to use #dataviz to explore complex biological data, make sure you’ve applied for this course by 9 March: www.ebi.ac.uk/training/eve... Some financial assistance is available, please see the course website for more information. 🧪🧬🖥️📊 #GeneSky

We're once again hosting the Human #Microbiome conference at @embl.org, organized by Ami Bhatt, Nicola Segata, Mani Arumugam and Peer Bork! We always have a great lineup of speakers, so register now and think about an abstract to submit (abstract submission deadline in June)

📣 Explore cutting-edge breakthroughs in microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. Join #EESMicrobiome!🦠 📅 16 – 19 Sep 2025 📍 EMBL Heidelberg and Virtual 📥 Submit your abstract by 24 June ➡️ https://s.embl.org/ees25-08-bl

We're hiring a postdoc!🚨 Study human-associated microbial communities in health & disease. 🔬Requirements: - PhD in bioinformatics, microbiology, or related field - Expertise in omics - Strong publication record Apply now!🌟 jobs.vib.be/j/69697/post... @vibmicrobes.bsky.social

Brochado and Maier labs in Germany are looking for a PhD student to study horizontal gene transfer in bacteria. ENDAMR Marie Curie doctoral network (endamr.eu) - an amazing opportunity to work with top scientists in the field all around Europe! www.cmfi.uni-tuebingen.de/mariecuriephd

The living world offers discoveries from bacteria to ecosystems, but how do we turn vast data into meaningful concepts? 🧬🌍 Join the 2nd edition of #EESTCBio to explore the interplay between theory and biology! 📥 Abstract deadline: 11 Feb 💻 s.embl.org/ees25-03-bl

Have computational biology skills and management experience? Want to make the world a better place by running of the most important archives of biological information in the world - ENA the DNA sequence archive? Working for @embl.org at @ebi.embl.org, based in Cambridge UK - this job is for you!

Post-doc opening to join our lab @ebi.embl.org to develop&apply #bioinformatics and #machine-learning methods to study intra-/extra cellular networks to extract disease mechanisms from #single-cell and #spatial multiomic data - please share 🙏 : embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

We have one postdoc position open with the Alliance Interinstitutional Postdoc Program. 🎈Details and applications here: 👇 health-life-sciences.de/opportunitie... 🎈Deadline: March 28, 2025, 5 pm CET. 🎈Project #128

In the beginning of the year, I moved to the Bio2Q Institute at Keio University in Tokyo (bio2q.keio.ac.jp). Really happy to be here and it's an amazing place to do microbiome research. We are looking for postdocs, so if you're interested please DM or email

#GastroEdPick Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations @cp-cell.bsky.social www.cell.com/cell/fulltex... #Gastrosky

Celebrating 25 years of @ensembl.bsky.social - the first announcement from @ewanbirney.bsky.social, milestone 1 was ensembl.org - thanks to all have worked on the resource, and the scientists who use it. Many exciting developments to present pangenomes, capture biodiversity and scale for the future

Very nice article in @nature.com about how bringing labs into the field is an incredible opportunity for environmental sciences & how it's a dream come true for many of us. Meet @nikobiota.bsky.social, head of @embl.org Mobile Labs. #protistsonsky #jcampubs www.nature.com/articles/d41...

We are delighted to announce The Health Privacy Challenge, an interactive opportunity for advancement at the intersection of computational biology and privacy research, brought to you as a part of CAMDA Conference at #ISMB/ECCB2025 🫐🍅 Register to participate: benchmarks.elsa-ai.eu?ch=4

Excited to share our opinion piece with the KC Huang Lab. Check it out here: Harnessing gut microbial communities to unravel microbiome functions doi.org/10.1016/j.mi... @typaslab.bsky.social