Stefanie Prast-Nielsen

Stefanie Prast-Nielsen

Assistant professor

Ass. Prof. in Metagenomics at the Centre for Translational Microbiome Research
PhD in Medical Biochemistry
My research focuses on the gut microbiota with emphasis on diet and the gut-brain axis

About me

I am Assistant Professor in Metagenomics 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, Python, R, Biostatistics as well as experience in project management, and good organizational and leadership skills.

Research description

At CTMR I am involved in projects dissecting the taxonomic and functional changes in the intestinal microbiota in various cohorts. 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. We find that relative abundance of Eubacterium rectale, Dialister and Bifidobacterium decrease along with several functions including metabolism of carbohydrates. We detected significant enrichment of Escherichia coli and the hemin transport system. Increased abundance of E. coli has been associated with inflammatory bowel disease and colorectal cancer and iron acquisition has recently been shown to be critical for bacterial pathogenicity. We thus raise concern about potential undesirable effects of the ketogenic diet on the gut microbiota and gut health and now aim to dissect the role of specific microbial taxa and genes/pathways for the anti-seizure effect of the ketogenic diet in a multi-omics approach to guide novel microbiota-targeted treatment strategies for epilepsy.

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


Current group members:

Stefanie Prast-Nielsen, Ph.D. Assistant Professor

Mauricio Barrientos-Somarribas, Ph.D. student

Aron Arzoomand, summer student 2019 (medical student, KI)

Alina Orozco, Research Trainee (Uppsala University)



Current (2019):

Swedish Brain Foundation, Margarethahemmet Society, Sunnerdahls Handikappfond, Jerringfonden 

Previous (2014-2018):

Margarethahemmet Society, Sunnerdahls Handikappfond, Linnea & Josef Carlssons Foundation, Karolinska Institutets Research Funds 


List of publications

Peer-reviewed articles

Lindefeldt M, Eng A, Darban H, Bjerkner A, Zetterström C, Allander T, Andersson B, Borenstein E, Dahlin M, Prast-Nielsen S. The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy. Nature Biofilms and Microbiomes. Jan;5(1):5 (2019)

Dahlin M and Prast-Nielsen S. The Gut Microbiome and Epilepsy. EBioMedicine 2019 Jun;44:741-746. doi: 10.1016/j.ebiom.2019.05.024. Epub May 31 (2019).

Fyhrquist N*, Muirhead G*, Prast-Nielsen S*, Jeanmougin M, Skoog T, Jules-Clement G, Feld M, Barrientos-Somarribas M, Pennino D, Suomela S, Tessas I, Lybeck E, Baran AM, Darban H, Singh Gangwar R, Gerstel U, Jahn K, Karisola P, Yan L, Hansmann B, Katayama S, Meller S, Bylesjö M, Hupé P, Levi-Schaffer F, Greco D, Ranki A, Schröder JM, Barker J, Kere J, Tsoka S, Lauerma A, Soumelis V, Nestle FO, Homey B, Andersson B, Alenius H. Microbe-host interplay in human skin homeostasis, atopy and autoimmunity. Accepted at Nature Communications (Aug 2019)*shared first authorship

Prast-Nielsen S, Tobin AM, Adamzik K, Powles A, Hugerth LW, Sweeney CM, Kirby B, Engstrand L, Fry L. Investigation of the Skin Microbiome: Swabs vs Biopsies. Br J Dermatology. DOI: 10.1111/bjd.17691, PMID: 30693476 (Jan 2019)

Prast-Nielsen S*, McNicholl AG*, O’Morain C, Megraud F, J Machado JC, Alarcon T, Leja M, Gasbarrini A, Andersen LP, Engstrand L† and Gisbert JP†. On behalf of the European Helicobacter and Microbiota Study Group (EHMSG; Comparison of the impact of Helicobacter pylori eradication treatment with bismuth and non-bismuth quadruple regimens on the gut microbiota. Under review at Microbiota in Health and Disease (Aug 2019). *Both authors equally contributed as first authors, † Both authors equally contributed as senior authors

Shi W, Hu Y, Zheng X, Ning Z, Wu M, Xia F, Prast-Nielsen S, Hu Y, Xu B. Longitudinal profiling of gut microbiome among tuberculosis patients under antituberculosis treatment in China: protocol of a prospective cohort study. Submitted to BMC Pulmonary Medicine (2019)

Prast-Nielsen S, Huang HH, Williams DL. Thioredoxin glutathione reductase: Its role in redox biology and potential as a target for drugs against neglected diseases. Biochim Biophys  Acta. Dec;1810(12):1262-71 (2011)

Prast-Nielsen S, Dexheimer T, SchultzL, StaffordWC, ChengQ, XuJ, JadhavA, Arnér  ESJ, SimeonovA. Inhibition of Thioredoxin Reductase by Porphyrins and Other Small Molecules Identified by a High Throughput Screening Assay. Free Radic Biol Med. May 1;50(9):1114-23 (2011)

Prast-Nielsen S, Cebula M, Pader I, Arnér ES. Noble metal targeting of thioredoxin reductase - covalent complexes with thioredoxin and thioredoxin-related protein of 14 kDa triggered by cisplatin. Free Radic Biol Med. 49(11):1765-78 (2010)

Eriksson SE, Prast-Nielsen S, Flaberg E, Szekely L, Arnér ESJ. High levels of thioredoxin reductase 1 modulate drug-specific cytotoxic efficacy. Free Radic Biol Med. 47(11):1661-71 (2009)

Rai G, Sayed AA, Lea W, Luecke H, Chakrapani H, Prast-Nielsen S, Jadhav A, Leister W, Shen M, Inglese J, Austin CP, Keefer L, Arnér ESJ, Simeonov A, Maloney DJ, Williams DL, Thomas CJ. Structure-Mechanism Insights and the Role of Nitric Oxide Donation Guide the Development of Oxadiazole-2-Oxides as Therapeutic Agents against Schistosomiasis. J Med Chem. 52(20):6474-83 (2009)

Anestål K, Prast-Nielsen S, Cenas N, Arnér ES. Cell Death by SecTRAPs: Thioredoxin Reductase as a Prooxidant Killer of Cells. PLoS ONE. 3(4):e1846 (2008)

Cenas N1, Prast S1, Nivinskas H, Sarlauskas J, Arner ES.Interactions of nitroaromatic compounds with the mammalian selenoprotein thioredoxin reductase and the relation to induction of apoptosis in human cancer cells. J Biol Chem. 281, 5593-603 (2006) 1shared first authorship

Enoksson M, Fernandes A, Prast S, Lillig C.H, Holmgren A, Orrenius S. Overexpression of glutaredoxin 2 attenuates apoptosis by preventing cytochrome c release. Biochem Biophys Res Commun. 327, 774-9 (2005)

Peer-reviewed conference contributions

Dahlin M, Lindefeldt M, Darban H, Bjerkner A, Zetterström C, Allander T, Andersson B, Prast-Nielsen S. The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with epilepsy. Poster and Abstract for the International Human Microbiome Consortium meeting 2018 (IHMC 2018), Killarney, Ireland; (2018)

Fyhrquist N, Andersson B, Kere J, Muirhead G, Prast-Nielsen S, Jeanmougin M, Barker J, Lauerma A, Homey B, Schröder J, Soumelis V, Nestlé F, Alenius H. Microbe-host interplay in atopic dermatitis and psoriasis: O801 Scandinavian Journal of Immunology 83 (5), 380-381 (2016)

Review articles (Peer-reviewed)

Dahlin M and Prast-Nielsen S. The gut microbiome and epilepsy, EBioMedicine, (2019)

Prast-Nielsen S, Huang HH, Williams DL. Thioredoxin glutathione reductase: Its role in redox biology and potential as a target for drugs against neglected diseases. Biochim Biophys  Acta. Dec;1810(12):1262-71 (2011)

Teaching portfolio

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

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

“Cellular and Molecular Infection” (Bachelor Program)

“Infection and immunity” (Bachelor Program)


2005-2009 Ph.D.: Medical Biochemistry

Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Biophysics, Division of Biochemistry

Dissertation: "Exploring Thioredoxin Reductase as an Anticancer Drug Target"


1998-2004 Diploma/Master of Science: Human Biology

Ernst Moritz Arndt University, Greifswald, Germany

Graduated summa cum laude

Majored in Pharmacology/Toxicology

Minored in Biochemistry/Molecular Biology & Microbiology/Virology

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