Michael Zimmermann Lab

This work has been done in both our lab and the @zellerlab.bsky.social

In his thesis, he established a benchmark framework for low-biomass microbiome profiling and applied it to colorectal and liver cancers to systematically map intra-tumoral microbe–host associations.

Last month, @fabianspringer.bsky.social defended his PhD entitled "Integrative Multi-Omics Analyses of the Cancer Tissue Microbiome". He investigated how intra-tumoral bacteria relate to host tumor features across genomic, transcriptomic, and metabolic layers.

Congrats Dr. Springer! 🎈

Comprehensive GC–MS/MS Quantification of Gut Microbiota–Derived Metabolites Across Intestinal and Systemic Tissues | LCGC International To enable robust investigation of microbiota–host metabolic interactions, a targeted gas chromatography–tandem mass spectrometry (GC–MS/MS) method was developed and validated by a research group at the European Molecular Biology Laboratory (Heidelberg, Germany) for the simultaneous quantification of 120 chemically diverse gut microbiota–derived metabolites across multiple biological matrices. LCGC International recently spoke to Nikita Denisov and Michael Zimmermann, two of the authors of a paper resulting from this work.

LCGC International recently spoke to Nikita Denisov and Michael Zimmermann, two of the authors of the our recently published paper that enables robust investigation of microbiota–host metabolic interactions.

You can check the interview here:
www.chromatographyonline.com/view/compreh...

Rewiring of oncogenic signaling in #DrugResistance is a moving target. In our new study, we used biophysical phosphoproteomics to investigate #BRAF mutant cancer, linking phosphorylation changes to protein function and #MolecularMechanisms through #Multi-Omics integration.
tinyurl.com/funsignaling

Greetings from Anders Lauszus. He is a Lab technician in the making from the Business College of Aarhus in Denmark. He will be joining the Zimmermann lab on the logistical front and various research tasks with the lab.
@embl.org

🦠 We'd like to know what *you* find as the most important info in microbial-based assays.
Our goal is to establish **Minimum Information about Xenobiotics-Microbiome Biotransformation (MIX-MB)** to improve data exchange, exploration, reproducibility, and integration across diverse microbial niches.

Your feedback will ensure these standards reflect real-world research needs.

📢 Please share with colleagues and collaborators in the field!

#microbiome #metabolomics #xenobiotics #datastandards #openscience #NFDI4Microbiota #NFDI #EMBL

Supported by @nfdi4microbiota.bsky.social @embl.org 🤝

MIX-MB (Minimum Information about Xenobiotics-Microbiome Biotransformation) - Community Consensus Survey This survey aims to establish the Minimum Information about Xenobiotics-Microbiome Biotransformation (MIX-MB) reporting standards. As we move toward an era of AI-driven discovery, the structural and f...

🚨 Do you work on microbial-mediated biotransformation of chemical compounds?
🧪 We would value your input to help us develop a standardized reporting framework for Xenobiotics–Microbiome interactions!

👉 Take the short survey (6–8 min): forms.gle/JNATejDrV2LR...

⬇️ ⬇️ ⬇️

Babies share microbiomes at nursery A study shows that social interactions in the nursery have a huge impact on babies’ microbiome development and may facilitate rapid strain recovery after antibiotic treatment.

⭐Research highlight: Social interactions in the nursery have a huge impact on babies’ and toddlers' #microbiome development, according to a new paper in Nature
https://www.nature.com/articles/d41591-026-00006-6

We are delighted to welcome Alder (@alder-e.bsky.social) to our group!

They are joining the lab as a scientific trainee and will be assisting with the chemical profiling of TREC samples.
@embl.org @embltrec.bsky.social

We are happy to welcome Elisabete Morais as a new member of Metabolomics Core Facility at @embl.org 🎊
In her postdoctoral work, she will focus on the development and application of NMR-metabolomics in microbiome research 🔬🦠

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-...

Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites - Analytical and Bioanalytical Chemistry The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....

📍Our paper is out!📍

Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives.
Check it out!

link.springer.com/article/10.1...

@Vanessa Pahl and @Richard Jacoby presented their work on marine chemical pollution

Greetings from the TREC Symposium, which gathered people from EMBL and beyond to share collected results and data! Lot's of interesting science has already been shown over the past days! Our lab presented work on marine chemical pollution. We are excited for the talks today! @embltrec.bsky.social

An hourglass with DNA bases, set in front of a Neanderthal skull, with a map in the background showing human migration patterns, superimposed with a few cave paintings. Image Credit: Daniela Velasco/EMBL

Nobel laureate Svante Pääbo, Director at the Max Planck Institute for Evolutionary Anthropology in Leipzig, will deliver the 2026 EMBL Kafatos lecture.

The lecture will explore how traces of Neanderthal DNA might shape human biology and health today.

www.embl.org/news/embl-an...

It’s not only medications—environmental chemicals can also inadvertently harm our gut microbes. Excited to have contributed a bit to this important study!

Microbiome Join us for a symposium exploring the critical role of the microbiome in health, disease, and therapeutic innovation. Leading experts will present cutting-...

Next week at #microbiome (a symposium exploring the critical role of the microbiome in health, disease, and therapeutic innovation) in Frankfurt 🇩🇪

Nicola Segata will talk about the microbiome in nutrition and cardiometabolic health.

Full program here: gsh.idloom.events/microbiome/p...

Are you a chemical biologist? Meet experts and peers at 'Chemical biology 2026' to discuss topics ranging from tool development to biological applications and from computational protein design to new drug modalities. ⚗️🧬 #EMBOChemBio
📅 8 – 11 Sep
📩 Submit abstract by 2 Jun: s.embl.org/chb26-01-bl

Bacterial networks #BacNet26 in September 2026 will be chaired by @lalouxlab.bsky.social and co-chaired by @s-lab.bsky.social with @coralietesseur.bsky.social

Sneak peak on invited speakers and preliminary program:
meetings.embo.org/event/26-bac...

You only have one more week to submit your abstract for 'Collectivity in living systems: emergence, function, and evolution' 👉 s.embl.org/ees26-01-bl

Don't miss #EESCollectivity which will explore how collective behaviours arise from fundamental principles across biological systems🦠🐒🧬

Happy to see our HT-PELSA paper now published in @natsmb.nature.com 🎊 Big thanks for the constructive review process! 📖Read the manuscript here (www.nature.com/articles/s41...) & check the thread for additional information ⬇️

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

🐝🦠 New paper: rdcu.be/eOf7A
Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

Vitamin B2 Production by Vaginal Lactobacilli Promotes Symbiosis The human vaginal microbiome, particularly with lactobacilli as the main inhabitants, plays a key role in maintaining women’s health. While lactic acid-mediated pathogen exclusion is well known, broad...

Proud to announce a new preprint of our lb - deep dive into #immune #metabolomic mode of action of the #vaginalmicrobiome - thanks to Isala! Great collab with @zimmermannlab.bsky.social & almost entire PhD of @carolinedricot.bsky.social combined in one manuscript www.biorxiv.org/content/10.1...

Vitamin B2 Production by Vaginal Lactobacilli Promotes Symbiosis The human vaginal microbiome, particularly with lactobacilli as the main inhabitants, plays a key role in maintaining women's health. While lactic acid-mediated pathogen exclusion is well known, broad...

We are very happy to share a new preprint 🎉

Congratulations to everyone involved!
@carolinedricot.bsky.social, @denisemselegato.bsky.social, @sarahlebeer.bsky.social and co.

www.biorxiv.org/content/10.1...

@velasevic.bsky.social

After exploring Europe’s coastlines, EMBL’s TREC expedition is moving inland! 💧

The new Traversing Ecosystems phase focuses on freshwater habitats – studying how human activity and environmental change affect life at the molecular level.

www.embl.org/news/science...

Looking for a new approach to studying or eliminating phages? Check out our study introducing anti-phage ASOs (antisense oligos) out in @Nature today. nature.com/articles/s4158…

This semester, we also welcomed Luka, the newest PhD candidate of the Zimmermann group!

Luka is coming from Montenegro and will work on high-throughput exploration of the metagenomic sequence space.

Welcome🎉🎊