MEM F811
Murtenstrasse 35
CH-3008 Bern
Tel. +41 31 632 98 42
jakob.zimmermannextra@unibe.ch
Recently, our group was able to demonstrate that bacterial metabolites from the maternal intestinal microbiota direct the development of the offspring’s innate immune system (Gomez de Agüero, Ganal-Vonarburg et al., Science, 2016). However, it remains elusive how this early microbial priming impacts on an individual’s later life physiology and disease susceptibility. In this project, we aim to identify the pervasive consequences of maternal microbial priming on the offspring’s host-microbiota mutualism.
Our group could previously elucidate the dynamics of IgA responses using the auxotrophic E. coli strain HA107 that can be grown in vitro but does not persist in vivo because it lacks critical enzymes for cell wall synthesis (Hapfelmeier et al., Science, 2010). In this project, I aim to develop novel auxotrophic bacterial strains to shed light on the immunological and metabolic host responses to diverse bacteria in a defined gnotobiotic colonization model.
During my PhD I developed a novel flow cytometric approach to interrogate the intestinal microbiota that relies on high sensitivity measurement of bacterial DNA content and light scattering characteristics in collaboration with the environmental research center Leipzig (Zimmermann, Hübschmann et al., Eur J Immunol, 2016). In this project we aim to further develop this approach to enable the sorting of live bacteria in the context of defined model floras such as the sDMDMm2 (stable defined moderately diverse mouse microbiota - Brugiroux et al., Nature Microbiology, 2016 and Uchimura et al., Genome Announcements, 2016)
2023 - ongoing Principal Investigator
2023 ERC Starting Grant “GuT Memory”
2023 SNSF Starting Grant “GuT Memory"
October 2021 – 2023: Staff scientist
Department for BioMedical Research, University of Bern, Switzerland
Prof. Andrew Macpherson, MD PhD
„Genetic engineering of gut symbionts to elucidate the dynamics of microbiota-directed immune responses"
Jun 2016 – Oct 2021: Postdoctoral fellow
Department for BioMedical Research, University of Bern, Switzerland
Prof. Andrew Macpherson, MD PhD
„The Role of the Maternal Microbiota in Shaping the Offspring’s Host-Microbiota Mutualism“ and "Record-seq sentinel cells for noninvasive assessement of gut function"
Jan 2016 – May 2016: Postdoctoral fellow
German Rheumatism Research Center Berlin, Germany
Prof. Dr. Andreas Radbruch,
“The Interplay of T-bet and ROR-γt for the Differentiation of T Helper Cell Lineages”
May 2011 – Dec 2015: PhD thesis
German Rheumatism Research Center Berlin, Germany
Prof. Dr. Andreas Radbruch,
“The Role of Th1, Th17 & Th17+1 Cells in the Induction & Perpetuation of Inflammatory Bowel Disease”
June 2010 – Jan 2011: Diploma thesis
Institute for Medical Microbiology & Hygiene, University of Freiburg, Germany
Prof. Dr. med. Andreas Diefenbach,
„The Role of Interleukin 22 in the Development of Colitis-Associated Cancer“
Sep 2009 – Jun 2010: Research assistant
Institute for Medical Microbiology & Hygiene, University of Freiburg, Germany
Prof. Dr. med. Andreas Diefenbach,
„The Role of Interleukin 22 in Acute and Chronic Intestinal Inflammation”
Jan 2009 – Mar 2009: Intern student
Center for Molecular Biology “Severo Ochoa”, University of Madrid, Spain
Prof. Dr. Francisco Sobrino
“Function of Non-Structural Proteins 3A and 3B for Replication of Foot-and-Mouth- Disease Virus”
Oct 2006 – Nov 2007: Student assistant
Institute for Molecular Medicine & Cell Research, University of Freiburg, Germany
Prof. Dr. Thomas Reinheckel
“Proteomic Analysis by Two-Dimensional Gel Electrophoresis”
Oct 2005 – Feb 2011: Study course ‘molecular medicine’
University of Freiburg, Germany
2023 ECCO Young Researcher Award
2023 DBMR Best Publication in 2022 award
2023 Co-awardee of Gastroenterology prize to Andrew Macpherson by Swiss Society for Gastroenterology
2022 AAI Bright Spark award by the German Society for Immunology
2022 Novartis Young Investigator Project Grant
2021 Young Investigator Project Grant by Bern Center for Precision Medicine
2020 Marylou-Ingram scholarship of the International Society for Advancement of Cytometry
2017-2019 Marie-Skłodowska-Curie Individual Fellowship for Postdoctoral Researchers
2011-2014 DFG PhD fellowship GRK1121
2011-2015 Member of the ZIBI graduate school Berlin
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