dr. Ellen De Paepe (PhD)

My research aims to understand how dietary and environmental exposures interact with the gut microbiome and human metabolism to influence health and disease, with a particular interest in exposures occurring early in life. Children are exposed to a rapidly changing mixture of dietary and environmental factors while their metabolic, immune and microbial systems are still developing. Understanding the molecular consequences of these exposures may help identify modifiable factors that contribute to disease later in life.
My research combines metabolomics and lipidomics with microbiome and other molecular data to obtain an integrated view of these interactions. My work initially focused on gastrointestinal disease in children and subsequently expanded towards adolescent metabolic health and the early-life exposome. I am now extending this research by integrating exposure assessment and multi-omics with DNA adductomics, to investigate whether modifiable dietary or environmental exposures can alter microbial and metabolic processes that promote chronic intestinal inflammation, impaired barrier function or DNA damage. 
Ultimately, I aim to identify early molecular signatures and mechanisms linking modifiable exposures to later disease risk, providing a scientific basis for prevention strategies before irreversible disease develops. Within CRIG, I want to combine our expertise in integrative metabolomics/lipidomics and DNA adductomics with complementary cancer expertise to develop this emerging research line at the interface of the exposome, gut health and cancer prevention.
 

Ellen De Paepe obtained her Master of Veterinary Medicine (option Research) at Ghent University in 2016 and an FWO-funded PhD in Veterinary Sciences in 2022, investigating paediatric cow’s milk allergy using integrative metabolomics and microbiome approaches. Since 2023, she works as a postdoctoral fellow at the Laboratory of Integrative Metabolomics (LIMET, Ghent University), where her research has expanded towards paediatric metabolic health and exposomics through several projects.
Her research combines high-resolution mass spectrometry, metabolomics/lipidomics, microbiome data and multi-omics integration. In 2026, she undertook a research stay at the International Agency for Research on Cancer (IARC, Lyon) to further develop expertise in DNA-adductomics data analysis and its application to cancer-relevant exposure research.
 

• A Validated Multi-Matrix Platform for Metabolomic Fingerprinting of Human Urine, Feces and Plasma using Ultra High-Performance Liquid-Chromatography coupled to Hybrid Orbitrap High-Resolution Mass Spectrometry. Analytica Chimica Acta, 2018. (PMID: 30172316)
• Ultra-High-Performance Liquid Chromatography Coupled to Quadrupole Orbitrap High-Resolution Mass Spectrometry for Multi-Residue Screening of Pesticides, (Veterinary) Drugs and Mycotoxins in Edible Insects. Food Chemistry, 2019. (PMID: 31151600)
• A Systematic Review of Metabolic Alterations Underlying IgE-Mediated Food Allergy in Children. Molecular Nutrition & Food Research, 2021. (PMID: 34648231)
• Integrated Gut Metabolome and Microbiome Fingerprinting Reveals that Dysbiosis Precedes Allergic Inflammation in IgE-Mediated Pediatric Cow's Milk Allergy. Allergy, 2024. (PMID: 38193259)
• A Repository of the Salivary Metabolome and its Key Drivers in 1,436 European Children. eBioMedicine, 2025. (PMID: 41223785)
• DNA Adduct Profiling of In Vitro Colonic Meat Digests to Map Red vs. White Meat Genotoxicity. Food and Chemical Toxicity, 2018. (PMID: 29458163)
• Microbiome and metabolome dynamics during radiotherapy for prostate cancer. Radiotherapy and Oncology, 2023. (PMID: 37827280)
• Dose-Dependent Microbiome, Metabolome and Lipidome Shifts in a Mouse Model of Colitis-Associated Colorectal Cancer using Azoxymethane and Dextran Sodium Sulphate. Animal Microbiome, 2026. 
   

• Lab address: Laboratory of Integrative Metabolomics, Salisburylaan 133, 9820 Merelbeke  
• Lab website  
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• Bibliography
• Ellen De Paepe is interested to receive invitations for presentations and talks