Michael Zimmermann Lab
@zimmermannlab.bsky.social
We use high-throughput MS, bacterial genetics, gnotobiology & computational models to study metabolic interactions in microbial ecosystems
@EMBL
Homepage: https://www.embl.org/groups/zimmermann/
@EMBL
Homepage: https://www.embl.org/groups/zimmermann/
Pinned
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
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
Reposted by Michael Zimmermann Lab
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 ⬇️
November 5, 2025 at 10:15 AM
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 ⬇️
Reposted by Michael Zimmermann Lab
🐝🦠 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
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
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...
www.nature.com
November 4, 2025 at 8:36 PM
🐝🦠 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
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
Reposted by Michael Zimmermann Lab
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...
www.biorxiv.org
November 2, 2025 at 6:46 AM
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...
Congratulations to everyone involved!
@carolinedricot.bsky.social, @denisemselegato.bsky.social, @sarahlebeer.bsky.social and co.
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...
www.biorxiv.org
October 29, 2025 at 4:13 PM
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...
Congratulations to everyone involved!
@carolinedricot.bsky.social, @denisemselegato.bsky.social, @sarahlebeer.bsky.social and co.
www.biorxiv.org/content/10.1...
Reposted by Michael Zimmermann Lab
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...
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...
October 23, 2025 at 9:02 AM
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...
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...
Reposted by Michael Zimmermann Lab
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…
September 10, 2025 at 3:40 PM
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🎉🎊
Luka is coming from Montenegro and will work on high-throughput exploration of the metagenomic sequence space.
Welcome🎉🎊
October 22, 2025 at 4:52 PM
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🎉🎊
Luka is coming from Montenegro and will work on high-throughput exploration of the metagenomic sequence space.
Welcome🎉🎊
Reposted by Michael Zimmermann Lab
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
#EESSymbiosis #ProtistsOnSky #SymbioSky
@hassansalem.bsky.social @berasymbionts.bsky.social @embl.org
The cellular mechanics of symbiosis: sensing friend from foe
www.embl.org
September 29, 2025 at 8:15 AM
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
#EESSymbiosis #ProtistsOnSky #SymbioSky
@hassansalem.bsky.social @berasymbionts.bsky.social @embl.org
Reposted by Michael Zimmermann Lab
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 🧵👇
Evolution of gut microbiota across honeybee species revealed by comparative metagenomics
Nature Communications - Here, the authors perform metagenomic analysis of honeybee gut microbes, uncovering many previously unidentified species and host specific differences in composition and...
rdcu.be
October 14, 2025 at 7:04 PM
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! 🎉
Welcome to the team! 🎉
October 16, 2025 at 8:40 AM
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! 🎉
Welcome to the team! 🎉
Reposted by Michael Zimmermann Lab
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...
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...
October 13, 2025 at 7:48 AM
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...
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...
Sneak peek: 2 weeks ago, our team presented the GUT-BASE: our new atlas mapping how gut microbes transform drugs.
We profiled thousands of microbe–drug interactions across gut species as a first step toward understanding — and eventually predicting — how the microbiome shapes drug metabolism.
We profiled thousands of microbe–drug interactions across gut species as a first step toward understanding — and eventually predicting — how the microbiome shapes drug metabolism.
October 7, 2025 at 1:26 PM
Sneak peek: 2 weeks ago, our team presented the GUT-BASE: our new atlas mapping how gut microbes transform drugs.
We profiled thousands of microbe–drug interactions across gut species as a first step toward understanding — and eventually predicting — how the microbiome shapes drug metabolism.
We profiled thousands of microbe–drug interactions across gut species as a first step toward understanding — and eventually predicting — how the microbiome shapes drug metabolism.
📍Paper alert 📍
Our new preprint is available on: chemrxiv.org/engage/chemr...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.
Our new preprint is available on: chemrxiv.org/engage/chemr...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.
Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites
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....
chemrxiv.org
September 24, 2025 at 12:21 PM
📍Paper alert 📍
Our new preprint is available on: chemrxiv.org/engage/chemr...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.
Our new preprint is available on: chemrxiv.org/engage/chemr...
Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.
Job Alert!
📍Postdoctoral Fellow - NMR-based metabolomics📍
The Metabolomics Core Facility (MCF) is seeking a Postdoctoral Researcher to expand our expertise in NMR-based metabolomics and contribute to both service provision and method development.
Info: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
📍Postdoctoral Fellow - NMR-based metabolomics📍
The Metabolomics Core Facility (MCF) is seeking a Postdoctoral Researcher to expand our expertise in NMR-based metabolomics and contribute to both service provision and method development.
Info: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Postdoctoral Fellow - NMR-based metabolomics
Your group The European Molecular Biology Laboratory (EMBL) is a top-ranked scientific research organization aimed at exploring the secrets of life. With over 1800 employees across six European sites,...
embl.wd103.myworkdayjobs.com
September 3, 2025 at 12:34 PM
Job Alert!
📍Postdoctoral Fellow - NMR-based metabolomics📍
The Metabolomics Core Facility (MCF) is seeking a Postdoctoral Researcher to expand our expertise in NMR-based metabolomics and contribute to both service provision and method development.
Info: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
📍Postdoctoral Fellow - NMR-based metabolomics📍
The Metabolomics Core Facility (MCF) is seeking a Postdoctoral Researcher to expand our expertise in NMR-based metabolomics and contribute to both service provision and method development.
Info: embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
We are hiring!
📍Scientific Officer - Metabolomics Core Facility📍
The MCF at @embl.org Heidelberg is seeking a new team member to support both routine metabolomics analyses and the development of new protocols and workflows.
Info:
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Closing Date: 29/09/25
📍Scientific Officer - Metabolomics Core Facility📍
The MCF at @embl.org Heidelberg is seeking a new team member to support both routine metabolomics analyses and the development of new protocols and workflows.
Info:
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Closing Date: 29/09/25
Scientific Officer - Metabolomics Core Facility
The European Molecular Biology Laboratory (EMBL) is a top-ranked scientific research organization aimed to explore the secrets of life. With over 1800 employees across six European sites, EMBL integra...
embl.wd103.myworkdayjobs.com
September 3, 2025 at 12:32 PM
We are hiring!
📍Scientific Officer - Metabolomics Core Facility📍
The MCF at @embl.org Heidelberg is seeking a new team member to support both routine metabolomics analyses and the development of new protocols and workflows.
Info:
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Closing Date: 29/09/25
📍Scientific Officer - Metabolomics Core Facility📍
The MCF at @embl.org Heidelberg is seeking a new team member to support both routine metabolomics analyses and the development of new protocols and workflows.
Info:
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
Closing Date: 29/09/25
Do you have experience in metabolomics/lipidomics/exposomics?
Check out the EMBL ARISE2 Fellowship Programme!
🔗 www.embl.org/training/ari...
📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI
🔗 www.ebi.ac.uk/people/perso...
📌 Applications close soon!
📆 30/09/2025
More info below👇
Check out the EMBL ARISE2 Fellowship Programme!
🔗 www.embl.org/training/ari...
📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI
🔗 www.ebi.ac.uk/people/perso...
📌 Applications close soon!
📆 30/09/2025
More info below👇
August 1, 2025 at 2:04 PM
Do you have experience in metabolomics/lipidomics/exposomics?
Check out the EMBL ARISE2 Fellowship Programme!
🔗 www.embl.org/training/ari...
📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI
🔗 www.ebi.ac.uk/people/perso...
📌 Applications close soon!
📆 30/09/2025
More info below👇
Check out the EMBL ARISE2 Fellowship Programme!
🔗 www.embl.org/training/ari...
📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI
🔗 www.ebi.ac.uk/people/perso...
📌 Applications close soon!
📆 30/09/2025
More info below👇
Reposted by Michael Zimmermann Lab
Wrap up on #EESMicrobiology @embl.org | @embo.org last week: grateful for the chance to give a talk and share some of our latest work — amazing science and even better people 🧫✨
July 2, 2025 at 5:40 PM
Wrap up on #EESMicrobiology @embl.org | @embo.org last week: grateful for the chance to give a talk and share some of our latest work — amazing science and even better people 🧫✨
Come check out the talk from Mariia, postdoc in our lab, at #EESMicrobiology today!
Great to be at #EESMicrobiology and excited to present later today (11.15!) our work in the framework of Microbial Ecosystems Transversal Theme @embl.org 🦠💊
🔬✨ Ready for a week full of cutting-edge microbiology research? Welcome to #EESMicrobiology Day 1!
Stay tuned for symposium highlights and some great pics of our speakers and participants 👀📸
🚀 We’re excited for a busy and inspiring week ahead!
Stay tuned for symposium highlights and some great pics of our speakers and participants 👀📸
🚀 We’re excited for a busy and inspiring week ahead!
June 25, 2025 at 7:37 AM
Come check out the talk from Mariia, postdoc in our lab, at #EESMicrobiology today!
🎓 Congratulations to Dr. Amber Brauer on successfully defending her PhD thesis, “Metabolic Interactions in the Entero-Hepatic Cycle,” supervised by Dr. Michael Zimmermann and Prof. Dr. Anne-Claude Gavin. Thesis Committee: Prof. Pascale Vonaesch and Prof. Mirko Trajkovski.
#Metabolomics #Microbiome
#Metabolomics #Microbiome
May 22, 2025 at 8:38 AM
🎓 Congratulations to Dr. Amber Brauer on successfully defending her PhD thesis, “Metabolic Interactions in the Entero-Hepatic Cycle,” supervised by Dr. Michael Zimmermann and Prof. Dr. Anne-Claude Gavin. Thesis Committee: Prof. Pascale Vonaesch and Prof. Mirko Trajkovski.
#Metabolomics #Microbiome
#Metabolomics #Microbiome
Call for #ARISE2 Fellowship Programme!
The Metabolomics Core Facility at EMBL Heidelberg is looking for a highly motivated person interested in developing computational pipelines for metabolomics data analysis and open data sharing.
www.embl.org/training/ari...
Call opening: 30 June
The Metabolomics Core Facility at EMBL Heidelberg is looking for a highly motivated person interested in developing computational pipelines for metabolomics data analysis and open data sharing.
www.embl.org/training/ari...
Call opening: 30 June
May 20, 2025 at 7:14 AM
Call for #ARISE2 Fellowship Programme!
The Metabolomics Core Facility at EMBL Heidelberg is looking for a highly motivated person interested in developing computational pipelines for metabolomics data analysis and open data sharing.
www.embl.org/training/ari...
Call opening: 30 June
The Metabolomics Core Facility at EMBL Heidelberg is looking for a highly motivated person interested in developing computational pipelines for metabolomics data analysis and open data sharing.
www.embl.org/training/ari...
Call opening: 30 June
Our group postdoc @zmahnoor.bsky.social, was invited as a guest on "The Knowledge Catalyst" podcast to speak about her experience with Reproducibility in Metabolomics Computational Workflows and the Implementation of the FAR principles. Check out the episode at: www.embl.org/about/info/o...
🚀 Launch alert! We're proud to introduce The Knowledge Catalyst, a new open science podcast from EMBL’s Open Science Community. 🎙️
Link to our first episode here: www.embl.org/about/info/o...
#OpenScience #FAIR #Metabolomics #Reproducibility #KnowledgeCatalyst #OpenSource @EMBL
Link to our first episode here: www.embl.org/about/info/o...
#OpenScience #FAIR #Metabolomics #Reproducibility #KnowledgeCatalyst #OpenSource @EMBL
May 14, 2025 at 8:11 AM
Our group postdoc @zmahnoor.bsky.social, was invited as a guest on "The Knowledge Catalyst" podcast to speak about her experience with Reproducibility in Metabolomics Computational Workflows and the Implementation of the FAR principles. Check out the episode at: www.embl.org/about/info/o...
Today, at the MSB unit seminar, our MSCA postdoc Anoop Singh spoke about quorum-sensing mediated bacterial interactions and biofilm formation in CRC-associated bacteria.
His findings aim to provide insights into CRC development and aid in developing therapeutics against pathogenic biofilms.
His findings aim to provide insights into CRC development and aid in developing therapeutics against pathogenic biofilms.
March 28, 2025 at 3:37 PM
Today, at the MSB unit seminar, our MSCA postdoc Anoop Singh spoke about quorum-sensing mediated bacterial interactions and biofilm formation in CRC-associated bacteria.
His findings aim to provide insights into CRC development and aid in developing therapeutics against pathogenic biofilms.
His findings aim to provide insights into CRC development and aid in developing therapeutics against pathogenic biofilms.
Reposted by Michael Zimmermann Lab
Bacteria can influence how sugars modify proteins in the brain – shown for the first time by EMBL researchers.
In their study, the scientists describe a new method to study glycosylation systematically & quantitatively, leading to new biological insights. 🧪🧠📈
www.embl.org/news/science...
In their study, the scientists describe a new method to study glycosylation systematically & quantitatively, leading to new biological insights. 🧪🧠📈
www.embl.org/news/science...
February 10, 2025 at 10:17 AM
Bacteria can influence how sugars modify proteins in the brain – shown for the first time by EMBL researchers.
In their study, the scientists describe a new method to study glycosylation systematically & quantitatively, leading to new biological insights. 🧪🧠📈
www.embl.org/news/science...
In their study, the scientists describe a new method to study glycosylation systematically & quantitatively, leading to new biological insights. 🧪🧠📈
www.embl.org/news/science...
Curious about how gut bacteria can modulate signatures in the brain?
Check out our new collaboration paper that shows how gut bacteria can influence the molecular pattern of glycosylation!
All data can be interactively explored 🖥️ apps.embl.de/glycoapp/.
Check out our new collaboration paper that shows how gut bacteria can influence the molecular pattern of glycosylation!
All data can be interactively explored 🖥️ apps.embl.de/glycoapp/.
February 10, 2025 at 12:30 PM
Curious about how gut bacteria can modulate signatures in the brain?
Check out our new collaboration paper that shows how gut bacteria can influence the molecular pattern of glycosylation!
All data can be interactively explored 🖥️ apps.embl.de/glycoapp/.
Check out our new collaboration paper that shows how gut bacteria can influence the molecular pattern of glycosylation!
All data can be interactively explored 🖥️ apps.embl.de/glycoapp/.