Michael Zimmermann Lab

Zimmermann Lab is now on BlueSky! We are #microbiome #research lab @embl.org using high-throughput MS, bacterial genetics, gnotobiology & computational models to study metabolic interactions in #microbial ecosystems 🦠 🧫 Follow to learn more about our work, publications & job openings! #science

🦠 Curios about how pesticides are being modified by bacteria? Our ARISE fellow Richard Jacoby has recently presented his project accessing hundreds of molecules and their bacterial metabolites in PESTIBASE 🔗 It is all captured in the online resource pestibase.embl.org/ for free exploration!

That's a wrap on #EESMetabolicEco! 🙌 A huge thank you to all of our amazing participants, speakers, and organisers for an inspiring 4 days of discussions on the metabolic interactions that shape ecosystems across every scale.

Great seminar from Kaili Fu from the Zimmermann group, who shared her postdoctoral work on gut microbiome-mediated drug-drug interactions in colorectal cancer treatment. Thanks, Kaili, for giving us a glimpse into this exciting work at the interface of microbiome research and cancer therapy!

🎓 Congratulations to Nikita Denisov on graduating! We’re delighted to celebrate this well-earned achievement and thank Nikita for his work and contributions, and for being a great colleague!

We are happy to welcome Pia Mozdzanowski, a visiting PhD student from the Ewald lab at EMBL-EBI. Her work focuses on inferring pesticide modes of action from image- and metabolomics-based screens in human cell lines. We’re excited for the exchange across metabolomics, imaging, and toxicology!

We are happy to welcome Guilherme Hernandez, a PhD student from the University of São Paulo, Brazil 🇧🇷. His research uses metabolomics and microbial biotransformation of bile acids to characterize breast milk bile acids and investigate their role in early-life gut microbiota maturation.

We welcome Kertu Liis in our lab! She is working on the microbiome-based detection of colon cancer in precancerous stages and on drug-microbiome interactions in Estonian Microbiome Cohort @tartumicrobiome.bsky.social

My first EMBL project uncovering synthetic steroid bacterial metabolism is now available publicly! My favourite part is the discovery of novel desmolase enzyme - see the preprint how we have found it 🧬💊🦠

We are happy to welcome @elboudlalihanane.bsky.social as a new member of the Zimmermann group at @embl.org 🎉 As part of @mmpu.bsky.social CRC project, she will focus on metabolomics and analytical method development, bringing her analytical chemistry expertise to support colorectal cancer research.

We welcome Leandro Presenza to the Zimmermann Lab 🎉 as a PhD student trainee. Leandro is a PhD candidate at University of São Paulo 🇧🇷. In his time @embl.org, he will focus on investigating the metabolome associated with postprandial metabolic responses using LC-MS.

We welcome Cecilia Cristina de Souza Rocha! Cecilia is a postdoctoral fellow at the University of São Paulo, Brazil 🇧🇷 and joins our group as a visiting researcher to investigate the role of the gut microbiota in the metabolism of antituberculosis drugs.

Exciting times at the Zimmermann Lab! We had a fantastic joint retreat with the EMIL group @jenspuschhof.bsky.social from DKFZ, filled with inspiring discussions, collaborative brainstorming, and plenty of science fun. Looking forward to new ideas and projects emerging from this great team-up!

Meet Tímea, who started recently as scientific officer at the metabolomics core facility @embl.org. Her work will focus on routine metabolomics and lipidomics analyses, developing new protocols and workflows, improving LC–MS methods, and supporting users. contact info: www.embl.org/groups/metab...

Excited to share the upcoming EMBO | EMBL Symposium “Metabolic interactions shape ecosystems” 🧬🌍 📍 Heidelberg & online 📅 21–24 July 2026 Abstract deadline: 14 April! More info & registration: www.embl.org/about/info/c... #Metabolism #Microbiome #SystemsBiology #Ecology #EMBL #EMBO

Excited to share the upcoming EMBO | EMBL Symposium “Metabolic interactions shape ecosystems” 🧬🌍 📍 Heidelberg & online 📅 21–24 July 2026 Abstract deadline: 14 April! More info & registration: www.embl.org/about/info/c... #Metabolism #Microbiome #SystemsBiology #Ecology #EMBL #EMBO

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

⭐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-...

📍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...

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!

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 ⬇️

🐝🦠 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

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...

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...

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…

Dear all, registration for the upcoming EMBO/EMBL Symposium on "the cellular mechanics of symbiosis" is now OPEN 🤩 ! Feel free to register ! www.embl.org/about/info/c... #EESSymbiosis #ProtistsOnSky #SymbioSky @hassansalem.bsky.social @berasymbionts.bsky.social @embl.org

Happy to announce that our comparative metagenomic analysis of the gut microbiota of five honeybee species - spearheaded by @aiswarya.bsky.social - is finally published in a peer-reviewed journal! rdcu.be/eKMCs @fbm-unil.bsky.social @dmf-unil.bsky.social 🧵👇

We would like to introduce Daniel who has just started his PhD with us, in which he aims to accelerate high-throughput metabolomics method development to uncover bidirectional interactions between drugs and the human gut microbiome in the context of health and disease. 🦠 Welcome to the team! 🎉

Excited to share our preprint led by Carlos Voogdt et al We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera. www.biorxiv.org/content/10.1...