My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org #microbiome #microsky doi.org/10.1128/msys...

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

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN. It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package. Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to... genomebiology.biomedcentral.com/articles/10....

Soo.... the last time it was online was April 1 2025 (consistently offline April 4 onwards) web.archive.org/web/20250401... My (limited) understanding is that hmpdacc.org is recently run by a team at IGS UMD, and the website being offline may or may not relate to changes at the NIH

This is in the replies and it demonstrates a real issue which is if you find profundity from an AI, you’re responding to something profound a human being wrote that was vacuumed up and what ends up happening is you thank AI and not only don’t thank the person, you have no idea they were involved

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

Professorship in Microbial Genetics @ University of Göttingen. Don't miss this chance to become my colleague! uni-goettingen.de/en/699057.html #SubtiWiki

Im so tired

We’re hiring a Postdoc on Gut Microbiome–Host Interactions @leibniz-hki.de, Jena 🇩🇪 You'll create organ-on-chip models to study how microbes mediate host responses to xenobiotics jobs.hki-jena.de/jobs/Postdoc...

We’re hiring a Postdoc in Gut Microbiome Metabolomics! Help us decode microbial metabolism and its impact on human health @leibniz-hki.de , Jena 🇩🇪 🔗 jobs.hki-jena.de/jobs/Postdoc...

Day 3 of popgen we talked about effective population size. No, I don't really understand it. You probably don't either. But I highly recommend this fantastic guide about how to think about Ne onlinelibrary.wiley.com/doi/10.1111/...

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 👇

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

Very excited to host the GRS Marine Microbes next year, which we are centering on three key themes: diversification, adaptation and resilience! Applications are now open - www.grc.org/marine-micro...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements. Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal. journals.asm.org/doi/10.1128/... 🧵

To all post-docs: The Genome Biology dept ‪@embl.org has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

Just out: metagenomics with internal standards yields phylogenetically resolved genome ("~cell") counts of bacteria, archaea, and photosynthetic eukaryotes per L of seawater, over the AMT29 Atlantic transect, via "single copy" genes (recA, radA, psbO). Compares with microscopy and flow cytometry.

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!

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms. www.medrxiv.org/content/10.1...

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...

TIL the EBV genome is *included in the hg38 assembly* so that EBV reads are not erroneously mapped elsewhere to the human genome. That's certainly .... an interesting solution ... 🤯 But it enabled this extremely cool work:

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems www.biorxiv.org/content/10.1... #jcampubs

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 🖥️🧬🦠

Spending some time in Germany at my parents' place after moving to Bio2Q / Keio University in Tokyo at the beginning of the year. Feels good to contemplate and find that's it was an awesome move. We have a few open positions at Postdoc level with lots of freedom and resources. DM if interested

Last year, I joined a brilliant group of researchers for a 3-week deep dive into host–microbe systems. Each week explored a different theme, led by inspiring lecturers. I’m excited to share that videos of their talks — along with presentations by several team members — are now on YouTube:

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper www.nature.com/articles/s41... #jcampubs

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...

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....

Fresh off the presses in @currentbiology.bsky.social : Is the deuterostome clade an artefact? www.sciencedirect.com/science/arti... We (yours truly, Paschalis Natsidis, Laura Piovani and co-leads Paschalia Kapli and @maxjtelford.bsky.social) set out to try to answer this question. Why? (1/12)

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

Maybe not the most beautiful experiment in biology but certainly top ten. What are your nominees? 1/

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 🧵.

📢 REMINDER ‼️ AMC - Abstract submission deadline: June 30, 2025 The Aging and Microbiome Conference 2025 #AMC2025 will take place from October 28-29, 2025 in #Jena. Join us for the latest developments and exciting discussions on #microbiome & #aging. 📅 amc25.leibniz-fli.de/registration/

Novel Research in Biological Artificial Intelligence: Expressions of interest and nominations for a Max Planck Director to lead research in the field of Biological Artificial Intelligence @mpi-cbg.de and @csbdresden.bsky.social. More information: www.mpi-cbg.de/news-outreac...

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

The rare microbial biosphere harbors many chemosensitive microorganisms undetectable by regular shotgun metagenomics. We can now explore them using our custom target-capture sequencing approach. Impressive work by Claudia Sanchis, part of her PhD thesis! www.biorxiv.org/content/10.1...

1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....

Powerful stuff from @juliosaezrod.bsky.social who found himself on the other end of the process - as a patient not a computational biology researcher - giving him insight into both research and patient perspectives. Huge credit to Julio for talking about his experiences here

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI doi.org/10.1080/1949...

“Historically, no one lived past age 35” "I’ve heard *so* many versions of this claim, including recently from a menopause doctor (implying menopause is not “natural” because noone lived long enough to go through it). Every time someone states this “fact,” a demographer loses a piece of their soul"

PHLAME: A benchmark for continuous evaluation of host phenotype prediction from shotgun metagenomic data https://www.biorxiv.org/content/10.1101/2025.06.12.658885v1

📥 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

I heard this morning that my informatics colleague Dr. Atul Butte passed after a battle with cancer. He was a giant in the field & inspired many of us over his distinguished career. He was a passionate champion of the power of big data & his impact on our field is immeasurable. RIP Atul & thanks.

For those of you who may not have known him, Dr. Atul Butte, a pioneer in informatics, was the winner of the 2024 Morris F. Collen award, a pinnacle achievement in our field, as part of his storied career. His passing is a major loss to us all. RIP Dr. Butte #MedSky

Atul Butte died yesterday. The world lost a giant. A big bear of a man. With a huge smile. With love for everyone. With energy that could power a room. I loved everything about Atul. I loved how he was always happy. I loved how excited he was about science and helping people.

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss www.pnas.org/doi/abs/10.1... #jcampubs 🌊