Stefanie Prast-Nielsen

My research aims to understand why epilepsy develops and why treatments work differently from one patient to another. I investigate the hypothesis that biological processes beyond the brain—including the gut microbiome, metabolism, inflammation, pharmacogenetics and other systemic factors—can influence both the risk of developing epilepsy and the response to treatment. By integrating nationwide Swedish health registers, prospective patient cohorts and multi-omics analyses, my research seeks to identify previously unknown risk factors, uncover biological mechanisms and contribute to more effective prevention and precision medicine for people with epilepsy.

I am Associate Professor (Docent) in Medical Microbiology and Senior Research Specialist in Multiomics, Machine Learning and Data Integration at the Department of Clinical Neuroscience, Karolinska Institutet.

My research combines epidemiology, multi-omics, machine learning and bioinformatics to address fundamental questions in epilepsy and other neurological diseases. I lead interdisciplinary research programmes that integrate nationwide Swedish health registers with prospective patient cohorts and advanced biological analyses to investigate disease development, treatment response and the role of biological processes beyond the brain.

Before joining the Department of Clinical Neuroscience in 2024, I was based at the Centre for Translational Microbiome Research (CTMR), where my research focused on the gut microbiome, dietary interventions and the microbiota–gut–brain axis. Today, my work builds on this foundation while expanding towards precision medicine, pharmacoepidemiology and data-driven discovery of previously unknown determinants of neurological disease.

My methodological expertise includes epidemiology, biostatistics, bioinformatics, machine learning and multi-omics data integration. I have extensive experience leading multidisciplinary collaborations and developing large-scale translational research projects.

My research focuses on understanding why epilepsy develops and why treatments work differently between patients. Rather than studying the brain in isolation, I investigate how biological processes beyond the brain contribute to disease development and treatment response.

My research is organized into three complementary programmes:

Using nationwide Swedish health registers and machine learning, we identify previously unknown risk factors and biological processes associated with epilepsy development, providing a foundation for prevention and future mechanistic studies.

A prospective nationwide cohort investigating how the gut microbiome, inflammation, pharmacogenetics and other biological factors influence

treatment response and disease progression in newly diagnosed epilepsy.

A prospective multi-omics programme investigating why ketogenic diet therapy is highly effective in some children with drug-resistant epilepsy while others derive limited benefit, with the aim of improving patient selection and identifying future therapeutic targets.

Through national and international collaborations, I also investigate the role of the microbiome in multiple sclerosis, Alzheimer’s disease and post-traumatic epilepsy, as well as during dietary interventions such as the ketogenic diet and modified Atkins diet.

Funding

• Swedish Brain Foundation
• Margarethahemmet Society
• Sunnerdahls Handikappfond
• Jerringfonden
• Linnea and Josef Carlssons Foundation
• Karolinska Institutets Research Funds
• ALF Medicin
• Epilepsifonden

I contribute to undergraduate, master’s and doctoral education at Karolinska Institutet, with a particular focus on microbiology, translational medicine and host–microbiome interactions.

I am co-organizer of the PhD course Biomedical Ecology – The Microbiota in Health and Disease (since 2021) and teach in courses within the Medical Programme, the International Master’s Programme and the Bachelor’s Programme.

I also supervise master’s and doctoral students in bioinformatics, microbiome research and neuroepidemiology, with projects spanning epilepsy, multiple sclerosis and dementia.