Stefanie Prast-Nielsen

About me

I am a 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.

Research description

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 here identified specific signatures of gut microbes and the immune system. Our findings may guide novel microbiota-targeted treatment strategies for epilepsy.

In addition, I have 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 & Josef Carlssons Foundation, Karolinska Institutets Research Funds

 

List of publications

Peer-reviewed articles

Nyström N, Prast-Nielsen S, Correia M, Globisch D, Engstrand L, Schuppe Koistinen I,  Halfvarson J. Mucosal and plasma metabolomes in new-onset paediatric inflammatory bowel disease: correlations with disease characteristics and plasma inflammation protein markers, Journal of Crohn's and Colitis, 2022;, jjac149, https://doi.org/10.1093/ecco-jcc/jjac149, PMID: 36219554

Nannapaneni P, Sundh J, Prast-Nielsen S, Rhedin S, Örtqvist Å, Naucler P, Henriques-Normark B. Metatranscriptomics of nasopharyngeal microbiota and host distinguish between pneumonia and health. Am J Respir Crit Care Med. PMID: 35947760, doi: 10.1164/rccm.202203-0463LE (2022)

Dahlin M, Singleton SS, David JA, Basuchoudhary A, Wickström R, Mazumder R, Prast-Nielsen S. Higher levels of Bifidobacteria and tumour necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet. EBioMedicine 80:104061 PMID: 35598439 (2022)

Oláh P, Szlávicz E, Kuchner M, Nemmer J, Zeeuwen P, Lefèvre-Utile A, Fyhrquist N, Prast-Nielsen S, Skoog T, Serra A, Rodríguez E, Raap U, Meller S, Gyulai R, Hupé P, Kere J, Levi-Schaffer F, Tsoka S, Alexander H, Nestle FO, Schröder JM, Weidinger S, van den Bogaard E, Soumelis V, Greco D, Barker J, Lauerma A, Ranki A, Andersson B, Alenius H, Homey B. Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation. J Dermatol Sci. DOI: 10.1016/j.jdermsci.2022.04.007, PMID: 35537882 (2022)

Lefèvre-Utile A, Saichi M, Oláh P, Delord M, Homey B, Soumelis V; MAARS consortium (including Prast-Nielsen S). Transcriptome‐based identification of novel endotypes in adult atopic dermatitis.  Allergy DOI: 10.1111/all.15150 (2021)

Shi W, Hu Y, Zhu N, Xia F, Wu M, Hu Y, Prast-Nielsen S, Xu B. Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: A pilot study. International Journal of Infectious Diseases https://doi.org/10.1016/j.ijid.2021.08.064 (2021)

Hopson LM, Singleton SS, David JA, Basuchoudhary A, Prast-Nielsen S, Klein P, Senac S, Mazumder R. Chapter Five - Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application. Progress in Molecular Biology and Translational Science  (2020)

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 atopic dermatitis and psoriasis. Nature communications, 10(1), 4703 (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; www.helicobacter.org). Comparison of the impact of Helicobacter pylori eradication treatment with bismuth and non-bismuth quadruple regimens on the gut microbiota. Microb Health Dis (2019); 1: e145 *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 anti-tuberculosis treatment in China: protocol of a prospective cohort study. BMC Pulm Med 19, 211 (2019) doi:10.1186/s12890-019-0981-9

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, Schultz L, Stafford WC, Cheng Q, Xu J, Jadhav A, Arnér  ESJ, Simeonov A. 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)

List of general articles and book chapters

Hopson LM, Singleton SS, David JA, Basuchoudhary A, Prast-Nielsen S, Klein P, Senac S, Mazumder R. Chapter Five - Bioinformatics and machine learning in gastrointestinal microbiome research and clinical application. Progress in Molecular Biology and Translational Science  (2020)

Prast-Nielsen S and Cryan JF. The Microbiota-Gut-Brain Axis in Epilepsy. Book chapter in section 3 on Neurobiology of Epilepsies of the third edition of Epilepsy: A Comprehensive Textbook, Wolters Kluwer (in Press)

Review articles (Peer-reviewed)

Dahlin M and Prast-Nielsen S. The gut microbiome and epilepsy, EBioMedicine, https://doi.org/10.1016/j.ebiom.2019.05.024 (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 am co-organizer of the PhD course “Biomedical Ecology - The microbiota in health and disease (course 2861)”

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)

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

“Cellular and Molecular Infection” (Bachelor Program)

“Infection and immunity” (Bachelor Program)

 

Education

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