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 Centre for Translational Microbiome Research (CTMR), MTC, 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 both the Department of Cell and Molecular Biology (CMB) and Karolinska University Hospital. I joined the Centre for Translational Microbiome Research in 2017 where my main research activities focus on the gut microbiota in various diseases with emphasis on dietary interventions and the microbiota-gut-brain axis.

I have several years of work experience in next generation sequencing and bioinformatics analysis using LINUX/UNIX, R, Python, Biostatistics, Machine Learning and Multiomics Data Integration.

I also have experience as Principal Investigator and Team Lead.

At CTMR I am involved in projects dissecting the taxonomic and functional changes in the intestinal microbiota in various cohorts. My current projects combine metagenomics with other -omics data such as metabolomics and proteomics. I use machine learning algorithms to detect health or disease-associated signals in big data. My main focus is a cohort of children with severe, drug-resistant epilepsy that are treated with the ketogenic diet. Epilepsy is the most common chronic neurological disorder characterized by recurrent, unprovoked seizures. Here, we analyze how the intestinal microbiota composition and function changes after three months of treatment using whole metagenomic sequencing. Combining this data with inflammation proteomics, we have identified specific signatures of gut microbes and the immune system. Our findings may guide novel microbiota-targeted treatment strategies for epilepsy. 

I am PI of the EpiGUT study, a large, nationwide, longitudinal study of the fecal and oral microbiota of treatment-naive epilepsy patients.

I am responsible for data analysis for other microbiota-focused research projects within Women's and Children's Health including infant's microbiota-restoration interventions after C-section and building prediction models for adverse pregnancy outcomes using clinical data and metagenomics data.

I have previously been involved in studies of the gut microbiota in pediatric and adult IBD, autism, heart disease and antibiotic eradication of Helicobacter pylori infections, as well as studies involving the upper respiratory tract and skin microbiota.

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)