New publication in the Journal Nature Microbiology

| by Anke Trinkler

We are delighted to announce that the members of our Microbiome Dynamics Group within the Cluster of Excellence “Balance of the Microverse” have contributed to deciphering a mechanism that determines how our gut microbiome processes healthy plant compounds and thus provided an important building block to encourage this balance through targeted individual intervention.

Our latest publication " Gut microbiome-mediated transformation of dietary phytonutrients is associated with healthy outcomes" where a comprehensive, multi-database analysis linking gut microbial enzymes to the transformation of 775 phytonutrients from edible plants across 3,068 global public human microbiomes was conducted. In vitro validation highlights species like Eubacterium ramulus, revealing substantial interpersonal and geographical variation in phytonutrient biotransformation. Our machine-learning analysis on 2,486 public case–control microbiomes shows that enzyme abundances involved in phytonutrient modification can distinguish health status across several diseases, underscoring the potential for personalized, diet-guided interventions

By integrating diverse enzymatic reaction and health-benefit data with large-scale metagenomic datasets, we demonstrate how microbiome-encoded biotransformation potential correlates with health phenotypes and disease contexts. Using metagenomic and metatranscriptomic analyses in germ-free and specific-pathogen-free mice, we further validated the link between microbial enzymes and the anti-inflammatory activity of common edible plants.

Key Findings

  1. Global scope of phytonutrient biotransformation: Transformation of 775 plant phytonutrients is associated with enzymes encoded by diverse gut microbes across thousands of samples.
  2. Species-level validation: In vitro assays confirm biotransformation activity by gut bacteria, notably Eubacterium ramulus.
  3. Variability across individuals and regions: Biotransformation potential shows high interpersonal and geographical variability.
  4. Health-state discrimination via enzymes: ML models using microbial enzyme abundances related to phytonutrient modification distinguish health status in multiple disease contexts.
  5. In vivo validation of anti-inflammatory activity: Metagenomics and metatranscriptomics in SPF and germ-free mice support the association between microbiome-encoded enzymes and anti-inflammatory effects of edible plants.

Methods at a Glance

  • We integrated multiple databases containing enzymatic reactions and health-benefit information.
  • We analyzed 3,068 global public human microbiomes to map phytonutrient biotransformation.
  • We performed in vitro assays to validate activity of gut species (e.g., Eubacterium ramulus).
  • We built machine-learning models on 2,486 public case–control microbiomes to relate enzyme abundances to health status.
  • We used metagenomics and metatranscriptomics in specific-pathogen-free and germ-free mouse models to validate functional associations.

Significance for Health, Environment, and Society
These findings suggest that individual and regional dietary responses are partly shaped by microbiome-encoded biotransformation capabilities. This opens a path toward precision nutrition strategies that tailor plant-rich diets to a person’s microbial potential, with implications for disease prevention, therapeutic monitoring, and sustainable dietary guidelines.

About the Publication

MBD members Dr. Bastian Seelbinder, Dr. Ana Depetris Chauvin, Prof. Gianni Panagiotou, Yueqiong (Bernard) Ni (alumni) and Lu Zhang (alumni) and external collaborators contributed to the study. We are very grateful to all our collaborators and funding sources from the German agency DFG who make this work possible.

  • Journal: Nature Microbiology (Impact factor 19.4)
  • Publication Date: 3rd of December, 2025
  • DOI: https://doi.org/10.1038/s41564-025-02197-z
  • Open Access/Access Options: http://creativecommons.org/licenses/by-nc-nd/4.0/
  • Acknowledgments
    This work was supported by the DFG - Deutsche Forschungsgemeinschaft under the project "MICROVERSE" (EXC 2051 – Project-ID 390713860).

Original Publication

Zhang L#, Marfil-Sánchez A#, Kuo T-H, Seelbinder B, van Dam L, Depetris-Chauvin A, Jahn L J, Sommer M O A, Zimmermann M, Ni Y*, Panagiotou G (2025)*, Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes, NATURE MICROBIOLOGY
DOI: 10.1038/s41564-025-02197-z

# These authors contributed equally to this work.

* Corresponding authors

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