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
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.
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.
July 24, 2026 at 11:20 AM
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.
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!
July 22, 2026 at 1:15 PM
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’re delighted to celebrate this well-earned achievement and thank Nikita for his work and contributions, and for being a great colleague!
July 14, 2026 at 7:37 PM
🎓 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’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!
July 7, 2026 at 3:05 PM
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.
June 29, 2026 at 8:30 AM
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
June 8, 2026 at 9:27 AM
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
Reposted by Michael Zimmermann Lab
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 🧬💊🦠
Bacterial metabolism of synthetic steroids across ecosystems reveals diverse biotransformation products, reactions, and enzymes https://www.biorxiv.org/content/10.64898/2026.06.05.730323v1
June 8, 2026 at 7:39 AM
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.
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.
April 27, 2026 at 11:27 AM
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.
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.
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.
April 20, 2026 at 9:34 AM
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.
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.
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.
April 15, 2026 at 7:26 AM
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.
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!
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!
April 9, 2026 at 9:27 AM
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!
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...
contact info: www.embl.org/groups/metab...
April 1, 2026 at 11:44 AM
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...
contact info: www.embl.org/groups/metab...
Reposted by Michael Zimmermann Lab
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
📍 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
Metabolic interactions shape ecosystems
www.embl.org
March 16, 2026 at 7:10 AM
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
📍 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
📍 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
Metabolic interactions shape ecosystems
www.embl.org
March 16, 2026 at 7:10 AM
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
📍 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
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! 🎈
Congrats Dr. Springer! 🎈
February 18, 2026 at 11:19 AM
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! 🎈
Congrats Dr. Springer! 🎈
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...
You can check the interview here:
www.chromatographyonline.com/view/compreh...
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.
www.chromatographyonline.com
February 16, 2026 at 2:25 PM
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...
You can check the interview here:
www.chromatographyonline.com/view/compreh...
Reposted by Michael Zimmermann Lab
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
tinyurl.com/funsignaling
February 11, 2026 at 1:57 PM
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
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
@embl.org
February 10, 2026 at 7:45 AM
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
@embl.org
🚨 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...
⬇️ ⬇️ ⬇️
🧪 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...
⬇️ ⬇️ ⬇️
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...
forms.gle
February 9, 2026 at 1:05 PM
🚨 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...
⬇️ ⬇️ ⬇️
🧪 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...
⬇️ ⬇️ ⬇️
Reposted by Michael Zimmermann Lab
⭐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
https://www.nature.com/articles/d41591-026-00006-6
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.
www.nature.com
February 2, 2026 at 2:30 PM
⭐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
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
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
February 2, 2026 at 3:32 PM
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
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 🔬🦠
In her postdoctoral work, she will focus on the development and application of NMR-metabolomics in microbiome research 🔬🦠
January 26, 2026 at 10:06 AM
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 🔬🦠
In her postdoctoral work, she will focus on the development and application of NMR-metabolomics in microbiome research 🔬🦠
Reposted by Michael Zimmermann Lab
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-...
We extend our deepest condolences to his family, friends, and colleagues.
www.embl.org/news/people-...
January 22, 2026 at 7:40 AM
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-...
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...
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...
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....
link.springer.com
December 16, 2025 at 10:56 AM
📍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...
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...
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
December 3, 2025 at 8:21 AM
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