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EMBL Symposium: The Human Microbiome

Dates: 5th – 8th September 2025
Location: Heidelberg, Germany
Official Event Website: https://www.embl.org/about/info/course-and-conference-office/events/ees25-08/

Join Metabolon at this EMBL Symposium: The Human Microbiome

Metabolon is attending the 2025 EMBL Symposium: The Human Microbiome, an internationally recognized meeting focused on advancing microbiome science in health and disease. This annual event gathers leading experts in microbial ecology, host-microbe interaction, systems biology, and translational microbiome science to explore the latest research and advancements shaping the future of the field.

You will find Zoltan Bognar, Josh Simpson and Virginie Lambert in the exhibition area. Come by our table to learn more about how metabolomics is redefining microbiome research and unlocking actionable biological insights across host–microbe interaction, clinical translation, and microbial therapeutics.

Key Themes at EMBL Human Microbiome

EMBL Human Microbiome 2025 will showcase innovative research and emerging technologies across key focus areas such as:

  • Methodological advances in microbiome analysis
  • The human microbiome across biological age
  • The human microbiome’s response to nutrition and drugs
  • Host-microbe interactions
  • Integrative approaches in microbiome research
  • Microbiome-targeted therapeutics
  • Future outlook for microbiome research and translation

View the Scientific Programme

The Role of Metabolomics in Human Microbiome Research

Metabolomics offers a direct window into microbial activity by measuring the biochemical products of microbial metabolism, providing unmatched insight into microbial function, host-microbe interactions, and environmental influences. Unlike genetic profiling, which reveals microbial presence, metabolomics captures what microbes are actually doing — revealing their metabolic outputs and how they affect host biology.

By characterizing microbial metabolites and their systemic impact, metabolomics enables researchers to identify disease biomarkers, track therapeutic responses, and uncover functional differences between health and disease states. It plays a pivotal role in bridging taxonomy and function, helping translate microbiome science into actionable, clinical insight.

Metabolomics supports microbiome research in several key areas:

  • Functional Insights – Identify how microbial communities influence host physiology and uncover their specific metabolic contributions.
  • Biomarker Discovery – Detect and validate metabolite-based signatures linked to disease progression, therapeutic response, or microbial dysbiosis.
  • Therapeutic Target Identification – Reveal novel pathways and metabolites that can serve as actionable targets for drug development or microbiome-based therapies.

Find out more:

Workshop

Wednesday, 17th September
12:15 – 13:15

A Microbiome Toolkit for Multi-Omics Discovery

Meaningful discovery happens when quality data, careful interpretation, and intuitive technology come together to reveal clear insights from complexity. With a single sample submission, Metabolon’s Microbiome Research Solution can provide metagenomics, untargeted metabolomics, and absolute quantification of short-chain fatty acids. This comprehensive but flexible approach empowers users to tailor omics analyses to specific research objectives. Upon completion of sample analysis, users gain access to Metabolon’s Microbiome Tool for intuitive data exploration and interpretation. Built around the trusted Integrated Bioinformatics Platform (IBP), the Microbiome Tool unifies metagenomic, metabolomic, and phenotypic data within a code-less, accessible platform that simplifies complex analyses without compromising flexibility or analytical depth and rigor. From raw sequencing data to rich visualizations, the platform performs end-to-end processing without requiring manual intervention or custom engineering. Rather than focusing solely on taxonomic profiling or single omics correlations, this solution seamlessly connects microbial composition to functional metabolic activity. With this foundation in place, researchers are equipped from the outset to identify the microbes that differentiate sample groups, uncover community-level patterns, and investigate functional variation across taxonomic levels with confidence and ease. Whether the goal is mechanistic discovery or translational application, Metabolon’s Microbiome Tool offers the analytical power and user-friendly experience needed to translate microbiome data into actionable knowledge.

In this workshop, a Metabolon scientist will walk you through the platform and showcase real world case studies.

What you’ll learn:

  • Microbiome Research Solution Overview – How to configure and create metabolomic and metagenomic datasets into a single, harmonized project.
  • Metagenomics and Metabolomics Complementarity – What combining these two omic modalities can achieve.
  • Microbiome Analysis Tool – Demonstration of interactive QC, taxonomic profiling, clustering and correlation analysis, and rich visualizations inside IBP.
  • Integrative Multiomics – Using machine-learning to link microbial taxa with metabolite profiles for predictive modelling.
  • Biological Interpretation Service – How expert curated reports distil complex results into clear narratives and next step hypotheses.

Poster

Thursday, 18th September
17:10 – 19:10

A Microbiome Toolkit for Multi-Omics Discovery

Why visiting Metabolon’s booth at EMBL Human Microbiome 2025

Why Metabolon? | Metabolon

With 25 years of scientific expertise, over 4,000 publications, more than 15,000 completed projects, and the world’s largest curated metabolite reference library (with over 5,400 level 1 and level 2 annotated metabolites), Metabolon is the global leader in metabolomics.

Our platform is built on high-resolution mass spectrometry, rigorous quality controls, and deep biochemical knowledge that ensures accurate identification and quantification of metabolites across complex microbiome-related sample types.

To maximize the value of metabolomic data, Metabolon offers an Integrated Bioinformatics Platform tailored for microbiome applications. This platform enables researchers to go beyond taxonomy and understand microbial function by linking metabolite data with microbial gene expression, pathways, and host responses. It supports:

  • Multi-omics integration to combine metabolomics with metagenomics, proteomics, or transcriptomics data.
  • Visualization and annotation tools to interpret large, complex datasets and trace microbial-derived metabolites to functional pathways.
  • Machine learning and statistical models that uncover microbial activity patterns, biomarkers, and correlations with clinical outcomes.
  • Pathway and network analysis to identify microbe-host metabolic interactions and functional hotspots.

Designed for collaboration, our tools allow interdisciplinary teams to explore, compare, and interpret findings in real-time, driving deeper biological insight and more precise hypotheses.

Don’t stay behind – incorporate high-quality metabolomics analysis in your project. Book a meeting with the team by filling the form on this page!

In the meantime, feel free to browse some helpful microbiome resources:

Meet Metabolon’s Team at EMBL Human Microbiome

  • Zoltan Bognar — With over 25 years of experience in delivering innovative services and products across diverse research fields, Zoltan brings deep expertise and a proven track record to every collaboration. He specializes in cutting-edge preclinical and clinical analysis solutions, tailored to the needs of our academic and industry partners. As our dedicated contact for the DACH region, Zoltan combines scientific know-how with a customer-focused approach. Based in Berlin, he is committed to helping our clients achieve successful research outcomes
  • Dr Joseph Gardner — Dr. Joseph Gardner is an accomplished bioinformatics scientist specializing in metabolic modeling and multi-omics analysis. He joined the Metabolon team in 2023 to help develop bioinformatics tools and drive research into the field.
  • Virginie Lambert – With over 15 years of experience in the Biotechnology and Life Sciences industry, will be your point of contact at Metabolon in France and Belgium. She will assist you in finding the best solutions and advancing in metabolomics thanks to her expertise in various omics. Her knowledge of academic research and R&D in the industry, will give you access to high quality services that meet the standards of your R&D projects. Virginie is based in the Rouen region, Normandy

Let’s connect in Heidelberg, Germany to learn how our team can support your microbiome research – book a meeting with the team using the form on this page!

Learn More About the Event

Schedule a Meeting

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References

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2. Bryant, J.A., et al., The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome. Nat Med, 2026. 32(1): p. 186-196

3. McGovern, B .H., et al., SER-109, an Investigational Microbiome Drugto Reduce Recurrence After Clostridioides difficile Infection: Lessons Learned From a Phase 2 Trial. Clin Infect Dis, 2021. 72(12): p. 2132-2140.

4. Feuerstadt, P., et al., SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection. N Engl J Med, 2022. 386(3): p. 220-229.

5. Hu, Z., et al., Targeted metabolomics reveals novel diagnostic biomarkers for colorectal cancer. Mol Oncol, 2025. 19(6): p. 1737-1750.

6. Butler, F.M., et al., Vegetarian Dietary Patterns and Diet-Related Metabolites Are Associated With Kidney Function in the Adventist Health Study-2 Cohort. J Ren Nutr, 2025.

7. Stanford, J., et al., Metabolomic Profiling and Diet Quality Scoring in a Randomized Crossover Trial of Healthy and Typical Dietary Patterns. Mol Nutr Food Res, 2025 . 69(23): p. e70271.

8. O’Connor, L.E., et al., Metabolomic Profiling of an Ultraprocessed Dietary Pattern in a Domiciled Randomized Controlled Crossover Feeding Trial. J Nutr, 2023. 153(8): p. 2181-2192.

9. Fritsch, D.A., et al., Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea. BMC Vet Res, 2022. 18(1): p. 245.

10. Leal, L.N., et al., Preweaning nutrient supply improves lactation productivity and reduces the risk of culling in Holstein cows. J Dairy Sci, 2025. 108(6): p. 5875-5888.

11. Ahsin, M., et al., Soil and pasture health underlie improved beef nutrient density determined by untargeted metabolomics in Southern US grass finished beef systems. NPJ Sci Food, 2025. 9(1): p. 151.

12. Yin, W., et al., Plasma lipid profiling across species for the identification of optimal animal models of human dyslipidemia. J Lipid Res, 2012. 53(1): p. 51-65.

13. Porter, F .D., et al., Cholesterol oxidation products are sensitive and specific blood-based biomarkers for Niemann-Pick C1 disease. Sci Transl Med, 2010. 2(56): p. 56ra81.

14. Needham, B .D., et al., Plasma and Fecal Metabolite Profiles in Autism Spectrum Disorder. Biol Psychiatry, 2021. 89(5): p. 451-462

15. Li, C., et al., Estradiol and mTORC2 cooperate to enhance prostaglandin biosynthesis and tumorigenesis in TSC2-deficient LAM cells. J Exp Med, 2014. 211(1): p. 15-28.

16. Green, P.G., et al., Metabolic flexibility and reverse remodelling of the failing human heart. Eur Heart J, 2025. 46(25): p. 2422-2433.

17. Maekawa, H., et al., SGLT2 inhibition protects kidney function by SAM-dependent epigenetic repression of inflammatory genes under metabolic stress. J Clin Invest, 2025. 135(19).

18. Wu, D., et al., Integrated screens reveal that guanine nucleotide depletion, which is irreversible via targeting IMPDH2, inhibits pancreatic cancer and potentiates KRAS inhibition. Gut, 2026.

19. Schwerdtfeger, L.A., et al., Gut microbiota and metabolites are linked to disease progression in multiple sclerosis. Cell Rep Med, 2025. 6(4): p. 102055.

20. Wu, H., et al., Microbiome-metabolome dynamics associated with impaired glucose control and responses to lifestyle changes. Nat Med, 2025. 31(7): p. 2222-2231.

21. Jacobs, J.P., et al., Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement. Microbiome, 2021. 9(1): p. 236.

22. Pietzner, M., et al., Plasma metabolites to profile pathways in noncommunicable disease multimorbidity. Nat Med, 2021. 27(3): p. 471-479.

23. Faquih, T.O., et al., Robust Metabolomic Age Prediction Based on a Wide Selection of Metabolites. J Gerontol A Biol Sci Med Sci, 2025. 80(3).

24. Scherer, N., et al., Coupling metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and human traits. Nat Genet, 2025. 57(1): p. 193-205.

25. Holmes, Z.C., et al., Untargeted metabolomic analysis of human milk from healthy mothers reveals drivers of metabolite variability. Sci Rep, 2024. 14(1): p. 20827.

26. Titz, B., et al., Implications of Ocular Confounding Factors for Aqueous Humor Proteomic and Metabolomic Analyses in Retinal Diseases. Transl Vis Sci Technol, 2024. 13(6): p. 17.

27. Bloom, S.M., et al., Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation. Nat Microbiol, 2022. 7(3): p. 434-450.

28. Leimer, E.M., et al., Lipid profile of human synovial fluid following intra-articular ankle fracture. J Orthop Res, 2017. 35(3): p. 657-666.