Three days of interesting discussions and new insights into host–microbiome dynamics at #CSMicrobiome2026 in Bruges, organized by @cellpressevents.bsky.social Congratulations @arnauvich.bsky.social for presenting his poster: Uncovering gut microbiome dynamics through dense longitudinal sampling

New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/

It was a true pleasure to work with you on this, @krukowskihubert.bsky.social ! It’s wonderful to see your hard work recognized. A well-deserved milestone for a fantastic researcher!

Hubert Krukowski@krukowskihubert.bsky.social · 6mo ago

Proud to see this work out in the world! Papers like this are never a solo effort. Huge thanks to @arnauvich.bsky.social and @murielderrien.bsky.social for their invaluable input, feedback, and help bringing this project to life!

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

science.org

Highlighting another recent paper from the lab in Science Advances on engineering a gut probiotic to modulate GLP-1 levels and ameliorating colitis. Led by Leonie Brockmann & @carlottaronda.bsky.social . @columbiasysbio.bsky.social @columbiauniversity.bsky.social 🧬🦠💊 www.science.org/doi/full/10....

Engineered probiotic restores GLP-1 signaling to ameliorate fiber-deficiency exacerbated colitis

Engineered probiotic delivers bacterial peptide that enhances GLP-1 and restores barrier integrity in diet-modulated colitis.

science.org

New discovery in ulcerative colitis: a bacterial toxin that kills macrophages and increases inflammation, which could be the foundation for a new treatment science.org/doi/10.1126/... science.org/doi/10.1126/... @science.org

A bacterial toxin disarms gut defenses against inflammation

Macrophage-toxic bacteria from patients with ulcerative colitis worsen gut inflammation in mice

science.org

Back-to-back recognition! 💪🏼 A huge shoutout to Arnau @arnauvich.bsky.social and Jeroen Raes for once again making @clarivate.com global #HighlyCited2025 list! 🌍✨ @viblifesciences.bsky.social @vibmicrobes.bsky.social clarivate.com/highly-cited...

Clarivate Highly Cited Researchers 2025

The Highly Cited Researchers 2025 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...

clarivate.com

Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs. @quadraminstitute.bsky.social rdcu.be/eMmcT

Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs

Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...

rdcu.be

Another great day at #UEGWeek 2025! 🎉Congratulations to our colleague Jorge Vazquez Castellanos for presenting his exciting work on microbial dysbiosis, inflammation, and the gut–brain axis in IBS at the United European Gastroenterology Week in Berlin🇩🇪 @myueg.bsky.social @vibmicrobes.bsky.social

Huge congratulations to our colleague @arnauvich.bsky.social for presenting his research on FODMAP restriction and gut microbiota in IBS patients at United European Gastroenterology Week 2025 in Berlin🇩🇪👏! #UEGWeek @myueg.bsky.social @vibmicrobes.bsky.social

The most interesting report of the week (IMHO) 🧵

Eric Topol@erictopol.bsky.social · 12mo ago

New @nature.com The possibility that lithium deficiency is a driver of Alzheimer's disease. Experimental model shows Li depletion impedes amyloid clearance, and repletion in humans could be achieved with low doses nature.com/articles/s41...

www.nature.com/articles/d41...

New hope for Alzheimer’s: lithium supplement reverses memory loss in mice

Studies in rodents and humans suggest that low levels of the metal contribute to cognitive decline.

nature.com

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

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...

medrxiv.org

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n) www.sciencedirect.com/science/arti...

Global genetic structure of human gut microbiome species is related to geographic location and host health

The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

sciencedirect.com

🦠🧬🖥️ New Bakta DB v6.0 released! After a year, it was time for a Bakta database update - and it's a huge one: - IPS: 330.9M - PSC: 135.3M - PSCC: 37M doi.org/10.5281/zeno... 👇 1/6

Citation: www.sciencedirect.com/science/arti...

A designed synthetic microbiota provides insight to community function in Clostridioides difficile resistance

Clostridioides difficile, a major cause of antibiotic-associated diarrhea, is suppressed by the gut microbiome, but the precise mechanisms are not ful…

sciencedirect.com

Nature research paper: Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses https://go.nature.com/3XmyOPD

Macrophages recycle phagocytosed bacteria to fuel immunometabolic responses - Nature

Phagocytosed bacteria can serve as an alternative nutrient source for macrophages, influencing their metabolic and immune responses through the recycling of microbial components, with the process regulated by nutrient-sensing mechanisms and bacterial viability.

go.nature.com

Legitmately thrilled to share our latest work, in which @fernpizza.bsky.social solved an experimental challenge in plasmid biology as old as the field: measuring how plasmids compete and evolve within individual cells!

Fernando Rossine@fernpizza.bsky.social · last yr.

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...

A must-read for any microbiome researcher 🦠📐and a new addition to our #bestpractices series Planning and describing a microbiome data analysis by @amydwillis.bsky.social and @davidandacat.bsky.social www.nature.com/articles/s41...

Planning and describing a microbiome data analysis - Nature Microbiology

We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.

nature.com

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

Postdoctoral position in bioinformatics of the human gut microbiome - 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 clinical applications

jobs.vib.be

Excited to share our MicrobiomeBenchmarkData preprint, addressing compositional data analysis for microbiome DA. This Bioconductor package features 3 datasets with biological ground truths. Spoiler: simple methods like LEfSe, Wilcoxon, RNA-seq methods performed well www.biorxiv.org/content/10.1...

Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth

Previous benchmarking of differential abundance (DA) analysis methods in microbiome studies have employed synthetic data, simulations, and "real data" examples, but to the best of our knowledge, none ...

biorxiv.org

A big congratulations to our incredible team at RaesLab! We’re excited to share that two of our colleagues, Arnau @arnauvich.bsky.social and Jeroen, have been honored on the global #HighlyCited2024 researchers list by @Clarivate🤩🙌🏼 @viblifesciences.bsky.social clarivate.com/highly-cited...

Highly Cited Researchers | Clarivate

The Highly Cited Researchers 2024 list identifies and celebrates individuals who have demonstrated significant and broad influence in their fields of research. Through rigorous selection criteria and ...

clarivate.com

Although I'm not a big fan of individual recognitions in science- collaboration and teamwork are the real driving forces- I'm honored to be recognised as #HighlyCited2024 by Clarivate. Grateful to all colleagues, mentors and collaborators who made this happen.