Stefanie Prast-Nielsen

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

I have a PhD in Medical Biochemistry from the Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet and spent several years as a Postdoc in Bioinformatics at the Department of Cell and Molecular Biology (CMB), KI (2011-2015), Karolinska University Hospital (2015-2017) an thed at Department of Microbiology, Tumor and Cell Biology (MTC), KI (2017).

In 2018 I became Assistant Porfessor at CTMR (Centre for Translational Microbiome Research) where my main research activities focused on the gut microbiota in various diseases with emphasis on dietary interventions and the microbiota-gut-brain axis.

In 2023, I became Docent (Associate Professor) in Medical Microbiology at CTMR. In 2024 I transitioned to the Department of Clinical Neuroscience, to the Neuroepidemiology group.

My current research focuses on large data analysis in epilepsy and other neurological diseases spanning from registry-based epidemiological studies to diverse omics datasets from patients and animal models. My main interest is the gut microbiota and how it influences the human body in neurological outcomes. I have several years of work experience in Biostatistics, Bioinformatics, Machine Learning and Multiomics Data Integration.

I also have experience as Principal Investigator and Team Lead.

My main research focus is epilepsy and other neurological diseases such as multiple sclerosis and Alzheimer’s disease. My expertise lies in big data analysis, from several omics datasets of both patients and animal disease models, to large registry data distinctly well-established in the Nordic countries. For this, we use state-of-the-art machine learning algorithms, advanced bioinformatics tools as well as classical biostatistical and epidemiologic methods.

My main research questions are:

How does the oral and gut microbiota influence epilepsy and anti-seizure treatment outcomes?

Current projects: 

EpiGUT

EpiDent

MAP-Keto (Microbial Associations and Prediction models for Ketogenic diet Epilepsy Treatment Outcomes)

How does exposure to commonly used drugs known to change the composition of the gut microbiota influence the risk of developing epilepsy?

Current project:

EpiGAST - a multinational epidemiological study building on our previous findings that exposure to proton pump inhibitors in early childhood increases the risk of epilepsy published here.

Uncovering the Hidden Half: Data-Driven Discovery of Unknown Epilepsy Risk Factors

Current project:

EpiRisk using machine learning algorithms to identify patterns in population based, real-world data of health care use prior to an epilepsy diagnosis.

Through both national and international collaborations, I also explore the microbiota in MS, Alzheimer’s disease, post traumatic brain injury and 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

I am co-organizer of the PhD course “Biomedical Ecology - The microbiota in health and disease (course 2861)” (since 2021)

I have previously taught seminars in Biochemistry for the Medical and Biomedical Program at KI (2005-2010) and I currently teach in the following courses:

“Biomedical Ecology - The microbiota in health and disease” (PhD level)

"Translational Physiology and Pharmacology" (International Master program)

"DSM2 (Den sjuka människan 2/Disease and Illness 2)" (Medical Program)

“Cellular and Molecular Infection” (Bachelor Program)

“Infection and immunity” (Bachelor Program)

Supervision:

Former Master students

Gustav Ahlström, UU, Thesis title: Metagenomic analysis of Crohn’s disease

Arissa Kitagishi, UU, Thesis title: The role of the gut microbiota in post-traumatic epilepsy

Nelly Mäkinen, UU, Thesis title: Investigation of the cross-talk between gut microbes and plasma metabolites in the development of post-traumatic epilepsy

Elin Rohdin, KI, Thesis title: Can the gut microbiota in babies born with C-section be restored?

Former PhD students (Co-supervisor)

Mauricio Barrientos-Somarribas; Thesis title: Tailoring bioinformatics strategies for the characterization of the human microbiome in health and disease

Current PhD students (Co-supervisor)

Karin Gustafsson, KI, Thesis title: The impact of novel epidemiological risk factors on neuroinflammation

Julia Krabbe, UU, Thesis title: Characterization of the gut and oral microbiomes and clinical correlates in dementia

Akash Bera, Open University, UK, Thesis title: Gut-to-brain communication in epilepsy: role in neuronal excitability and seizure pathophysiology