Management organigramme of the NCCR Microbiomes.


Director Jan Roelof van der Meer Environmental and Evolutionary Microbiology, University of Lausanne Lab website
Co-Director Julia Vorholt Microbial Physiology, ETH Zurich Lab website
Deputy Director Philipp Engel Host-associated Microbial Communities, University of Lausanne Lab website
Deputy Co-Director Emma Wetter Slack Food Immunology, ETH Zurich Lab website

Management team

Operational Manager Eavan Dorcey
Scientific and Technology Program Manager Robin Tecon

Principal Investigators

Martin Ackermann Microbial Systems Ecology, ETH Zurich Lab website
Rizlan Bernier-Latmani Environmental Microbiology, EPFL Lab website
Gilbert Greub Clinical Microbiology, Lausanne University Hospital (CHUV) Lab website
Benoît Guery Bacterial and Fungal Infections, Lausanne University Hospital (CHUV) Lab website
Siegfried Hapfelmeier Gut Microbiology, University of Bern Lab website
Wolf-Dietrich Hardt Salmonella Pathogenesis, ETH Zurich Lab website
Vassily Hatzimanikatis Computational Systems Biotechnology, EPFL Lab website
Christof Holliger Environmental Biotechnology, EPFL Lab website
Tadeus J. Kawecki Experimental Evolutionary Biology, University of Lausanne Lab website
Christoph Keel Pseudomonas Plant and Insect Interaction, University of Lausanne Lab website
Sara Mitri Evolutionary Ecology of Microbial Communities, University of Lausanne Lab website
Ian Sanders Ecology and Evolution of Symbiotic Organisms, University of Lausanne Lab website
Yolanda Schaerli Bacterial Synthetic Biology, University of Lausanne Lab website
Roman Stocker Environmental Microfluidics, ETH Zurich Lab website
Shinichi Sunagawa Microbiome Diversity and Functions, ETH Zurich Lab website
Christian von Mering Bioinformatics and Systems Biology, University of Zurich Lab website
Grégory Resch Phage and Phage-Lysin Therapy, Lausanne University Hospital (CHUV) Lab website
Pascale Vonaesch Microbiota-targeted Interventions, University of Lausanne Lab website
Alma Dal Co Microbial Interactions and Collective Behaviour, University of Lausanne Lab website

The NCCR Consortium

The NCCR Microbiomes is a consortium integrating 20 research groups from six institutions across Switzerland. The University of Lausanne (UNIL) acts as leading house, and ETH Zurich (ETHZ) as co-leading house. The NCCR is directed by Prof. Jan Roelof van der Meer (director, UNIL) and Prof. Julia Vorholt (co-director, ETHZ). Prof. Philipp Engel (UNIL) and Prof. Emma Slack (ETHZ) act as deputy director and co-director, respectively.

Six interlinked work packages (WP) tackle the research questions of the NCCR. Each WP gathers several research groups, with all groups being active across multiple WPs. One to two NCCR principal investigators (PIs) lead each WP and coordinate their efforts across the whole network.

The NCCR Microbiomes is managed by Dr. Robin Tecon (Programme Manager) and Dr. Eavan Dorcey (Operational Manager), who are in charge of the daily operations of the consortium, its scientific coordination, educational activities, knowledge and technology transfer, and equal opportunities.

The Steering Committee of the NCCR gathers the NCCR Direction, WP leaders and Operational and Programme managers. It coordinates research integration in close discussion with all Principal Investigators within the work packages, monitors research progress and difficulties, and advises on the use of shared or collective infrastructure.

A Scientific Advisory Board annually evaluates the NCCR, its research accomplishments, collaborations, knowledge and technology transfer, and education activities. The members of the Scientific Advisory Board are listed below.

All members of the NCCR Microbiomes constitute its General Assembly, which meets annually. The NCCR Ethical Committee is formed by PIs with translational research and clinical experience, and under the responsibility of the Programme Manager. It oversees the NCCR activities requiring coordination of ethical approval or more profound discussion of data and results dissemination or of societal implications of microbiome management.

Members of the NCCR Microbiomes Scientific Advisory Board

Prof. Willem de Vos Wageningen University & Research, The Netherlands Lab website
Prof. em. Dani Or ETH Zurich, Switzerland Lab website
Prof. Stefanie Widder University of Vienna, Austria Lab website
Prof. Paul Wilmes University of Luxembourg, Luxembourg Lab website
Dr. Olga Sakwinska Nestlé Research Center, Switzerland Lab website
Dr. Kiran Patil EMBL, Germany Lab website
Prof. Janet Jansson Pacific Northwest National Laboratory, US Lab website

NCCR Members

Andreas Keppler Probing plant microbiomes using a metabolomics approach PhD student Vorholt lab, ETHZ
Benjamin Daniel Elucidating colonization dynamics of the Arabidopsis thaliana microbiome PhD student Vorholt lab, ETHZ
Maxime Batsch Investigating microbial interactions and community assembly in soil communities using picoliter droplets cultivation PhD student van der Meer lab, UNIL
Swapan Preet Understanding how adaptive immune response influence stability of different components of the mouse intestinal microbiota PhD student Slack lab, ETHZ
Alessio Milanese Developing new approaches for the integrated analysis of multi-omics data from microbial communities Postdoc Sunagawa lab, ETHZ
Laëtitia Cardona Understanding processes leading to granular biofilm formation of the wastewater microbiome Postdoc Holliger lab, EPFL
Estelle Pignon Influence of metabolic and non-metabolic properties of engineered E. coli strains on spatial pattern formation in microbial communities PhD student Schaerli lab, UNIL
Melanie Stäubli Developing methods to predict growth rates of community members from metatranscriptomic data PhD student Sunagawa lab, ETHZ
Senka Causevic Exploring microbial community engineering from the perspective of bioaugmentation PhD student van der Meer lab, UNIL
Elliott Patelli Mathematical modelling and computational methods for analysis and engineering of microbiomes PhD student Hatzimanikatis lab, EPFL
Luca Beldi Microbiota-mediated processes driving and resolving Clostridioides difficile infection PhD student Hapfelmeier lab, UniBE
Olivier Schaeren In-vivo study of protective intestinal long-term colonization with microbiota-syntrophic strains of Salmonella typhimurium PhD student Hapfelmeier lab, UniBE
Mihai Danaila Increasing scalability, modularity and performance of the Microbe Atlas Project Scientific software developer von Mering lab, UZH
Audam Chhun Using synthetic biology to engineer the honey bee gut microbiota Postdoc Schaerli lab, UNIL
Elena Montenegro Borbolla Investigating human C. difficile infection PhD student Guery lab, CHUV
Evangelia Vayena Reconstruction and data-based analysis of metabolic networks in microbial communities PhD student Hatzimanikatis lab, EPFL
Yangji Choi Metagenomic analysis of microbiota in patients with SARS-CoV-2 infection PhD student Greub lab, CHUV
Omid Oftadeh Methods of data integration for the reconstruction of metabolic interactions in microbial communities and the analysis and design of their evolution in time PhD student Hatzimanikatis lab, EPFL
Alan Pacheco Exploring and engineering community interactions in the plant microbiome Postdoc Vorholt lab, ETHZ
Natalia Rodilla Role of Accumulibacter phosphatis (ACC) in the aerobic granular sludge community PhD student Holliger lab, EPFL
Ricardo Castilho The role of soil microbiome in plant-fungal interactions Postdoc Sanders lab, UNIL
Sedreh Nassirnia Strengths and limitations of metagenomics analyses in clinical microbiology PhD student Greub lab, CHUV
Jiangtao Qiao The emergent property of arsenic methylation in anaerobic paddy soil-derived microbiomes Postdoc Bernier-Latmani lab, EPFL
Daniel Weilandt Large scale kinetic models of microbes Postdoc Hatzimanikatis lab, EPFL
Birge Özel-Duygan Tracing microbes’ fingerprints using flow cytometry data Postdoc Greub lab, CHUV
Alyson Hockenberry Synthetic microbiomes as model systems to study the dynamics of host-associated communities and analyze the basis of disease resistance Postdoc Ackermann lab, ETHZ
Tania Miguel Trabajo Studying pairwise bacterial species interactions to predict the composition and dynamics of synthetic soil microbial communities PhD student van der Meer lab, UNIL
Silvia Moriano Gutierrez Revealing mechanisms of bacterial invasion of the bee gut microbiota Postdoc Engel lab, UNIL
Stefano Ugolini Microfluidic techniques for studying bacterial communities Postdoc Stocker lab and Ackermann lab, ETHZ
Daniel Garrido-Sanz Interactions between bacterial inoculants and the resident root-microbiome of crops Postdoc Keel lab, UNIL
Markus Arnoldini Understanding the metabolic host-microbiota interaction network using a simplified mouse gut microbiota Postdoc Slack lab, ETHZ
Jordan Vacheron Deciphering the Phage-bacteria interaction network in agricultural soils Postdoc Keel lab, UNIL
Disha Tandon Understanding long term evolution of live vaccine bacterial species in association with gut microbiota inside mammalian gastrointestinal tract PhD student Hapfelmeier lab, UniBE
Fergus Wright The role of the soil microbiome in plant-fungal symbiosis for improved crop production PhD student Sanders lab, UNIL
Anna Sintsova Bioinformatician Sunagawa lab, ETHZ
Carmen Chen Microbiota and host response in Salmonella Typhimurium infection PhD student Guery lab, CHUV
Hugo Sallet Deciphering microbial interactions in the paddy soil microbiome PhD student Bernier-Latmani lab, EPFL
Mathias Herzog Enterobacteriaceael competition in the gut of Mice and Man PhD student Hardt lab, ETH Zurich
Giorgia Greter Evaluating microbial population dynamics in the gut using a 3-membered microbiota PhD student Slack lab, ETHZ
Matthias Hülsmann Enhancing the productivity of the edible microalga Chlorella vulgaris by co-cultivation with designed microbial consortia PhD student Ackermann lab, ETHZ
Soon-Jae Lee Chronobiology of plant holobiont and mycorrhizal symbiosis Postdoc Sanders lab, UNIL
Oliver Meacock Do self-assembled patterns facilitate efficient division of labour in microbial communities? Postdoc Mitri lab, UNIL
Yassine Cherrak Characterization of an isolated commensal E.coli strain able to compete with Salmonella Typhimurium in vivo Postdoc Hardt lab, ETH Zurich
Yassine El Chazli Elucidating host-microbial metabolic cross-talk in the gut of the western honey bee apis mellifera PhD student Engel lab, UNIL
Andrew Quinn Elucidating host-microbial metabolic cross-talk in the gut of the western honey bee apis mellifera Postdoc Engel lab, UNIL

NCCR Alumni

Karen Viacava Arsenic methylation as an emergent properties in soil microbiomes Now at Institute of Geography, University of Bern