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Michael Zimmermann Lab

@zimmermannlab.bsky.social
566 followers 426 following 46 posts

We use high-throughput MS, bacterial genetics, gnotobiology & computational models to study metabolic interactions in microbial ecosystems @EMBL Homepage: www.embl.org/groups/zimmermann

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Michael Zimmermann Lab @zimmermannlab.bsky.social · 28/09/2026
🦠 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!
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EMBL Events @events.embl.org · 24/07/2026
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 22/07/2026
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!
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 14/07/2026
🎓 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!
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 07/07/2026
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!
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 29/06/2026
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 08/06/2026
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
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Mariia A. Beliaeva @mariiabeliaeva.bsky.social · 08/06/2026
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 🧬💊🦠
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 27/04/2026
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 20/04/2026
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 15/04/2026
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 09/04/2026
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!
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 01/04/2026
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/03/2026
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
embl.org
Metabolic interactions shape ecosystems
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/03/2026
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
embl.org
Metabolic interactions shape ecosystems
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 18/02/2026
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! 🎈
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/02/2026
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...
chromatographyonline.com
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.
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Savitski Lab @savitski-lab.bsky.social · 11/02/2026
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
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 10/02/2026
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
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 09/02/2026
🚨 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... ⬇️ ⬇️ ⬇️
forms.gle
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...
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Nature Medicine @natmed.nature.com · 02/02/2026
⭐Research highlight: Social interactions in the nursery have a huge impact on babies’ and toddlers' #microbiome development, according to a new paper in Nature www.nature.com/articles/d41591-026-…
nature.com
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 02/02/2026
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
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 26/01/2026
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 🔬🦠
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EMBL @embl.org · 22/01/2026
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-...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/12/2025
📍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...
link.springer.com
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....
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 03/12/2025
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
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EMBL @embl.org · 01/12/2025
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...
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
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Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · 26/11/2025
It’s not only medications—environmental chemicals can also inadvertently harm our gut microbes. Excited to have contributed a bit to this important study!
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Segata Lab @cibiocm.bsky.social · 26/11/2025
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...
gsh.idloom.events
Microbiome
Join us for a symposium exploring the critical role of the microbiome in health, disease, and therapeutic innovation. Leading experts will present cutting-...
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EMBL Events @events.embl.org · 20/11/2025
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
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Ákos T Kovács @evolvedbiofilm.bsky.social · 20/11/2025
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...
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EMBL Events @events.embl.org · 11/11/2025
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🦠🐒🧬
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Savitski Lab @savitski-lab.bsky.social · 05/11/2025
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 ⬇️
nature.com
High-throughput peptide-centric local stability assay extends protein–ligand identification to membrane proteins, tissues and bacteria - Nature Structural & Molecular Biology
Li et al. further develop a high-throughput peptide-centric local stability assay that speeds up sample preparation 100-fold and extends protein–ligand identification to membrane proteins, tissues and...
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Philipp Engel @pengellab.bsky.social · 04/11/2025
🐝🦠 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
nature.com
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...
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Sarah Lebeer @sarahlebeer.bsky.social · 02/11/2025
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...
biorxiv.org
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 29/10/2025
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...
biorxiv.org
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...
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EMBL @embl.org · 23/10/2025
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...
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Jörg Vogel @jorg-vogel-lab.bsky.social · 10/09/2025
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…
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 22/10/2025
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🎉🎊
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Flora Vincent @floravincent.bsky.social · 29/09/2025
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
embl.org
The cellular mechanics of symbiosis: sensing friend from foe
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Philipp Engel @pengellab.bsky.social · 14/10/2025
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 🧵👇
rdcu.be
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 16/10/2025
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! 🎉
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Typas Lab @typaslab.bsky.social · 13/10/2025
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 07/10/2025
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.
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 24/09/2025
📍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.
chemrxiv.org
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....
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 03/09/2025
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...
embl.wd103.myworkdayjobs.com
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,...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 03/09/2025
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
embl.wd103.myworkdayjobs.com
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...
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Michael Zimmermann Lab @zimmermannlab.bsky.social · 01/08/2025
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👇
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Mariia A. Beliaeva @mariiabeliaeva.bsky.social · 02/07/2025
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 🧫✨
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