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! 🙌

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…

sciencedirect.com

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...

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...

cell.com

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com : www.nature.com/articles/s41... See the linked threads for more details!

Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology

Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.

nature.com

Sebastian Schmidt@tsbschm.bsky.social · 12mo ago

We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social www.biorxiv.org/content/10.1...

Our review on the Japanese gut microbiome is now published! By analyzing >30,000 gut metagenomes from 37 countries🧬, we re-evaluated the unique feature of the Japanese gut microbiome🦠 in a global context🌏. doi.org/10.2183/pjab...

The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease

Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in t …

doi.org

我々の日本人の腸内マイクロバイオーム研究をまとめたレビュー論文が公開されました！ 先行研究の総括に加え、🌏世界37カ国・3万件超の大規模メタゲノムデータ🧬を用いて、日本人腸内マイクロバイオーム🦠の特徴を再評価しています。 doi.org/10.2183/pjab...

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

Viruses are found in almost every ecosystem across the planet. Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions. Learn more: www.embl.org/news/science...

Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social. academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007

VIRE: a metagenome-derived, planetary-scale virome resource with environmental context

Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr

academic.oup.com

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

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

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...

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

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...

The gut remembers: the long-lasting effect of medication use on the gut microbiome | mSystems

Over the past decades, medication use has steadily increased worldwide, with individuals frequently taking multiple medications (polypharmacy), often repeatedly over extended periods of time (1). Yet,...

doi.org

Full thread will come later, but @annacusco.bsky.social's preprint on the dog pet gut microbiome is out! Using ONT+Illumina, we get better MAGs than to corresponding species representative in public databases doi.org/10.1101/2025...

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

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

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...

biorxiv.org

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 🧵.

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · last yr.

A census of hidden and discoverable microbial diversity beyond genome-centric approaches https://www.biorxiv.org/content/10.1101/2025.06.26.661807v1

📥 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

Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field. rdcu.be/epoRR @blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.

Genomics of host–microbiome interactions in humans

Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...

rdcu.be

I’m pleased to share that I've joined the Life Science Data Research Center at the University of Tokyo as a Project Associate Professor today! Excited to return to Japan and start this new chapter in Kashiwa! I look forward to continuing my research and new collaborations!

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)

EMBL Events@events.embl.org · 2y ago

📣 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

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...

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...

nature.com

It is my pleasure to invite you to the first Ukrainian School in Evolutionary Biology (USEB), which will take place in Uzhhorod University from January 27 to 31, 2025. The event is hybrid. Primary target audience is high school, undergraduate, Msc and Phd students, but everyone is welcome.

Excited to share our study led by @SakenovaNazgul! We used chemical genetics to identify and understand cross-resistance & collateral-sensitivity (CS) between antibiotics and reduced AMR development with CS drug pairs @embl.org with @camille_goemans @EPFL_en www.nature.com/articles/s41...

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics - Nature Microbiology

Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. This study presents an approach to systematically discover and ...

nature.com

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 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.

embl.org

Excited to see this out in Cell! If you use microbiome data to look for disease associations, you might want to make sure microbial load is not confounding your results! www.cell.com/cell/fulltex... Congratulations @suguru-nishijima.bsky.social @borklab.bsky.social and others #microsky #microbiome

Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations

A machine-learning approach enables the quantification of microbial load (microbial cells per gram) in fecal samples based on the relative microbiome profile. The predicted microbial load emerged as a...

cell.com

Pleased to announce that our latest paper is published in Cell! We developed a novel ML model that predicts fecal microbial load from relative species profiles, revealing it as a key factor shaping gut microbiome variation and disease-microbe associations www.sciencedirect.com/science/arti...

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…

sciencedirect.com

Excited to share our latest preprint on a novel computational tool to predict fecal microbial load solely from relative species profiles! Our study revealed that fecal microbial load is a substantial confounder in microbiome-disease association studies. www.biorxiv.org/content/10.1...