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Daniel Podlesny

@podlesny.bsky.social
1.1K followers 784 following 12 posts

Postdoc @BorkLab.bsky.social @embl.org. PhD @UniHohenheim.bsky.social. Microbiome, HGT, FMT, Strain-level Metagenomics

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Reposted by Daniel Podlesny
Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/09/2026
We've been very moved by the tributes paid to Peer at conferences around the world: e.g. at ISME by Jeroen Raes, at ECCB by Christian von Mering, and at the Tara conference by Chris Bowler. Thank you! @isme-microbes.bsky.social @eccb-europe.bsky.social @taraoceans-science.bsky.social @raeslab.org
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Daniel Podlesny @podlesny.bsky.social · 11/06/2026
New paper out in @cp-cellhostmicrobe.bsky.social by our super talented predoc @jonas-bio.bsky.social Congrats!
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Reposted by Daniel Podlesny
Jonas Schiller @jonas-bio.bsky.social · 10/06/2026
Our new paper „Variations in the latitudinal diversity gradients of the ocean microbiome“ was just published in @cp-cellhostmicrobe.bsky.social 🥳 We present a global analysis of prokaryotic #biodiversity in the surface and mesopelagic layers of the ocean 🦠🌊 www.cell.com/cell-host-mi...
cell.com
Variations in the latitudinal diversity gradients of the ocean microbiome
Eriksson et al. conduct a global marine microbiome diversity analysis and demonstrate how the surface ocean latitudinal diversity gradient is disproportionately shaped by a few species-rich taxa. Mask...
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 01/06/2026
New in @natgenet.nature.com: a moving obituary for Peer. Francesca Ciccarelli, Jan Korbel & Christian von Mering reflect on his scientific vision, from protein domains and genome evolution to metagenomics, and on his generosity as a mentor and friend to so many. www.nature.com/articles/s41...
nature.com
Peer Bork (1963–2026) - Nature Genetics
Nature Genetics - Peer Bork (1963–2026)
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Marisa Isabell Keller @maelschermarisa.bsky.social · 01/06/2026
Our work exploring host-microbial co-metabolism of bile acids in patients with alcohol-related liver disease (ALD) has been published in the JHEP Reports: www.sciencedirect.com/science/arti... 🪐 A big thank you to everyone involved, to the GALAXY and MicrobLiver consortia who made this possible! 🙌
sciencedirect.com
Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism
Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-relat…
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Reposted by Daniel Podlesny
Chris Stewart @stewartlab.bsky.social · 18/03/2026
🚨 A new piece of the preterm gut microbiome puzzle just fell into place! Bifidobacterium metabolise human milk oligosaccharides (HMOs) in early life — shaping immunity, supporting gut development, and protecting against diseases like necrotising enterocolitis (NEC). www.nature.com/articles/s41...
nature.com
Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids - Nature Microbiology
Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of c...
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Lukas Malfertheiner @lukasmalf.bsky.social · 25/02/2026
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...
cell.com
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...
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Sebastian Schmidt @tsbschm.bsky.social · 25/02/2026
The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today: www.sciencedirect.com/science/arti...
sciencedirect.com
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems
Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…
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Chan Yeong Kim @chanyeong-kim.bsky.social · 09/02/2026
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.
cell.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...
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Reposted by Daniel Podlesny
Bork Group at EMBL Heidelberg @borklab.bsky.social · 09/02/2026
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!
cell.com
Planetary microbiome structure and generalist-driven gene flow across disparate habitats
A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...
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Reposted by Daniel Podlesny
EMBL @embl.org · 09/02/2026
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...
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 30/01/2026
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. 🧵
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/01/2026
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social. 📄 www.science.org/doi/10.1126/... 🌐 search.foldseek.com/foldmason 💾 github.com/steineggerla...
science.org
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
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Reposted by Daniel Podlesny
EMBL @embl.org · 22/01/2026
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-...
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Pedro Beltrao @pedrobeltrao.bsky.social · 16/01/2026
This is such hard news to process. Such an amazing scientist and inspiration for so many of us. www.embl.org/news/embl-an...
embl.org
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
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Arkadiy Garber @ironark.bsky.social · 30/11/2025
metaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...
academic.oup.com
metaTraits: a large-scale integration of microbial phenotypic trait information
Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is
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Daniel Podlesny @podlesny.bsky.social · 02/12/2025
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
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Cristina Legido-Quigley @legidoquigley.bsky.social · 24/07/2025
Super happy to share our latest preprint in #liverdisease & #gut microbiota mechanisms. www.medrxiv.org/content/10.1...
medrxiv.org
Alcohol-related liver disease disrupts bile acid synthesis and is associated with compensatory gut microbiota changes
Background: Alcohol overuse disrupts liver function and alters microbial gut communities, with alcohol-related liver disease (ALD) accounting for half of all liver-related deaths worldwide. Bile acids...
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Reposted by Daniel Podlesny
Bork Group at EMBL Heidelberg @borklab.bsky.social · 21/07/2025
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 🖥️🧬🦠
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Chan Yeong Kim @chanyeong-kim.bsky.social · 21/07/2025
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
biorxiv.org
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...
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Sebastian Schmidt @tsbschm.bsky.social · 27/06/2025
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 🧵.
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Jaime Huerta-Cepas @jhcepas.bsky.social · 25/06/2025
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...
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Ursula von der Leyen @vonderleyen.ec.europa.eu · 05/05/2025
Europe’s choice is clear. To put science at the heart of its economy. To become the home of scientific freedom and collaboration. And to welcome talent from all over the world. I’m glad to present the first elements of our Choose Europe Initiative. → europa.eu/!TTbWbJ
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Daniel Podlesny @podlesny.bsky.social · 28/04/2025
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.
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Michael Baym @baym.lol · 09/04/2025
Our latest paper, in which @brinda.eu (along with @zaminiqbal.bsky.social and others) introduces phylogenetic compression for storage and search of enormous microbial genome libraries, was published today in @naturemethods.bsky.social: rdcu.be/eg4OA 1/
rdcu.be
Efficient and robust search of microbial genomes via phylogenetic compression
Nature Methods - Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks.
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Michael Kreil @michaelkreil.bsky.social · 20/02/2025
Die Faschisten sind auf dem Vormarsch - schon wieder - und wir machen genau die gleichen Fehler - schon wieder. datajournal.org/schon-wieder/
datajournal.org
Schon wieder
Der Aufstieg der NSDAP/AfD
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Wählerwille des Grauens @mdbdesgrauens.bsky.social · 21/01/2025
Dass nur eine einzige Redaktion sich hier traut, zu schreiben, was jeder sehen konnte: "Musk macht Hitlergruß" – das ist so dystopisch, ihr werft uns denen zum Fraß vor.
Screenshot von Google News: Zeit Online schreibt von vermeintlichem Hitlergruß, NTV sagt Geste ähnelt, SZ von möglichem Hitlergruß, Welt spricht von römischen Gruß oder Geste von HerzenWeitere Screenshots von Google News. ZDF spricht von fragwürdiger Geste, T-Online schreibt Mast ihre Tiere mit Geste, BR schreibt von Hitlergruß ähnlicher Geste und so weiterWeitere Screenshots von anderen Medien im selben TonWeiteres Screenshots, diesmal aber mit Watson, die als einziges Medium den Hitlergruß als solchen benennen
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Mario Sixtus @sixtus.net · 21/01/2025
Die deutschen Mainstream-Medien sind soweit nach links gerutscht, dass sie einen Hitlergruß nicht mehr Hitlergruß nennen.
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Nature Reviews Genetics @natrevgenet.nature.com · 08/01/2025
NEW ONLINE! New online! A phylogenetic approach to comparative genomics
go.nature.com
A phylogenetic approach to comparative genomics
Nature Reviews Genetics, Published online: 08 January 2025; doi:10.1038/s41576-024-00803-0Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests.…
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Chan Yeong Kim @chanyeong-kim.bsky.social · 28/12/2024
I’m excited to share our new paper published in Nature Communications! In our work, we discovered TANB77, a bacterial clade previously obscured by a polyphyletic grouping in conventional taxonomy, as a reliable biomarker across diverse immunotherapy recipient groups. www.nature.com/articles/s41...
nature.com
A conserved pilin from uncultured gut bacterial clade TANB77 enhances cancer immunotherapy - Nature Communications
Here, the authors show that higher levels of the gut bacterial clade TANB77 associate with better response to cancer immunotherapy, and further demonstrate in mice that a conserved pilin from TANB77 p...
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Typas Lab @typaslab.bsky.social · 23/12/2024
Excited to share our preprint with @savitski_lab led by @tarabartolec.bsky.social, @KMitosch & Clément Potel! We uncovered a mechanism by which the T7 phage broadly counteracts DNA-targeting bacterial defenses by deploying a loose cannon kinase in its genome @embl.org www.biorxiv.org/content/10.1...
biorxiv.org
Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses
Bacteria and bacteriophages are in a constant arms race to develop bacterial defense and phage counter-defense systems. Currently known phage counter-defense systems are specific to (the activity of) ...
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Jotham Suez (SuezLab@JHU) @suez.bsky.social · 13/12/2024
🚨 New review in @natrevgastrohep.bsky.social: Should you take probiotics with antibiotics? www.nature.com/articles/s41... Bottom line: current evidence does not support the common perception that probiotics can facilitate the gut microbiome's recovery from antibiotics. BUT! 1/🧵
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Michael Fischbach @mfgrp.bsky.social · 11/12/2024
Today we report that an engineered skin bacterium, swabbed gently on the head of a mouse, can unleash a potent antibody response against a pathogen. Could lead to topical vaccines that are applied in a cream. @djenetbousbaine.bsky.social led the charge... @natureportfolio.bsky.social 1/55
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Svetlana Ugarcina Perovic @svetlanaup.bsky.social · 09/12/2024
If you missed #MVIF 34, no worries, here is Vedanth's talk and other amazing talks! www.youtube.com/watch?v=SnDy...
youtube.com
Vedanth Ramji - argNorm: Normalization of antibiotic resistance gene annotations to ARO | S04 MVIF34
YouTube video by Microbiome Virtual International Forum
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 05/12/2024
About one week left to apply! Open postdoc position for analysing environmental microbiome data, e.g. from @embl.org 's TREC expedition along the coastlines of Europe www.embl.org/about/info/t...
embl.org
TREC – An expedition to study coastal ecosystems and their response to the environment, from molecules to communities
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 13/11/2024
Hot off the press: "Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations" www.sciencedirect.com/science/arti... See below for @suguru-nishijima.bsky.social 's thread on the preprint! #microsky #microbiome
sciencedirect.com
Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations
The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative a…
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Michael Hoffman @michaelhoffman.bsky.social · 11/11/2024
1/AlphaFold 3 code now available, following researcher criticism for not providing it with the initial publication. www.nature.com/articles/d41...
nature.com
AI protein-prediction tool AlphaFold3 is now open source
The code underlying the Nobel-prize-winning tool for modelling protein structures can now be downloaded by academics.
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Jan Claesen @claesengroup.bsky.social · 19/10/2024
Hi everyone, I tried assembling a Microbiome & friends starter pack. 🦠🧫🔬 Still learning to use bluesky and might have missed you, let me know if you would like to be included. go.bsky.app/Fq36egy
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 07/11/2024
We're looking for a postdoc on the Computational Analysis of Environmental #Microbiome Data! www.embl.org/jobs/positio... In the past two years, #EMBL scientists have gathered more than 3000 soil, sediment and water samples from Europe's coastlines within the #TREC expedition. (1/4)
embl.org
EMBL Jobs
We offer a wide range of challenging scientific and non-scientific positions at all of our European locations and encourage applications from international candidates at all career levels.
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 23/10/2024
The first day of our lab retreat is underway. We didn't venture far from EMBL, just up the hill to Königstuhl overlooking Heidelberg and the Rhine valley. However, we did invite guest from other labs who are working on the microbiome and are enjoying the discussions across the groups!
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 15/08/2024
⚡️ Our latest preprint "Refined Enterotyping Reveals Dysbiosis in Global Fecal Metagenomes" led by @maelschermarisa.bsky.social is now available! We’ve revisited the concept of #enterotypes using a massive dataset of 16,772 human fecal #metagenomes from 38 countries! 🌍🧬 doi.org/10.1101/2024... 🧵
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Bork Group at EMBL Heidelberg @borklab.bsky.social · 07/08/2024
New paper: "Bifidobacterium and Lactobacillus Probiotics and Gut Dysbiosis in Preterm Infants: The PRIMAL Randomized Clinical Trial" showing that while the probiotics did not reduce the incidence of MDRO+, they modulated their microbiome toward eubiosis. jamanetwork.com/journals/jam... (1/2)
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