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 Mucosal Immunology, ETH Zurich Lab website

Management team

Operational Manager Eavan Dorcey
Scientific and Technology Program Manager Robin Tecon
Technology Transfer Advisor Sandra Sulser
Data Manager Kendra Brown

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
Tadeusz 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
Claire Bertelli Clinical Metagenomics, Lausanne University Hospital (CHUV) Lab website
Olga Schubert Microbial Systems Ecology, ETH Zurich 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

Associated Partners

Simon Van Vliet Systems ecology of bacterial biofilms, University of Basel Lab website
Adrian Egli Applied Microbiology Research, University of Zürich Lab website
Wenyu Gu Microbial Physiology and Resource Biorecovery, EPFL Lab website
Leyla Davis Curator Head of Research, Zoo Zürich Zoo Zürich

NCCR Coworkers

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
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 Postdoc Hapfelmeier lab, UniBE
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
Birge Özel-Duygan Tracing microbes’ fingerprints using flow cytometry data Postdoc Greub lab, CHUV
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 Senior Researcher 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
Andrew Quinn Elucidating host-microbial metabolic cross-talk in the gut of the western honey bee apis mellifera Postdoc Engel lab, UNIL
Julien Luneau Understanding how local interactions affect spatial dynamics and antibiotic response within E. coli community using microfluidics Postdoc Mitri lab, UNIL
Alessia Carrara Identification of biomarkers in clinical microbiology using genomics and metagenomics approaches PhD student Greub lab, CHUV
Jaime Gonzalez Evolutionary steps of environmental bacteria during initial adaptation to D. melanogaster gut Postdoc Kawecki lab, UNIL
Alessia Del Panta Collective behaviour in microbial communities PhD student Mitri lab, UNIL
Carla Hernández Cabanyero Molecular mechanisms involved in the interplay of the small intestinal microbiome with inflammation and nutrient absorption Postdoc Vonaesch Lab, UNIL
Laetitia Le Caous Live Salmonella vaccine and interactions with host ecosystem PhD student Hapfelmeier lab, UniBE
Hans-Joachim Ruscheweyh Bioinformatician Sunagawa lab, ETHZ
Youzheng Teo Role of ectopic colonisation by oral bacteria in undernourished children Research Staff Vonaesch lab, UNIL
Edoardo Mollica Biophysical interactions of microbial communities on the leaf surface PhD Student Stocker lab, ETHZ
Lea Fuchs Identification of metabolic pathways relevant for gut colonization in Salmonella Typhimurium PhD Student Hardt lab, ETHZ
Youn Henry Exploring the role of evolution in shaping host-microbiota interactions using the model species Drosophila melanogaster Postdoc Kawecki lab, UNIL
Sebastian Burz Probing interactomes of gut and environment communities by microfluidics in order to reveal mechanisms of microbiomes engineering Postdoc van der Meer lab, UNIL
Simon Yersin Role of the human gastrointestinal microbiota in childhood undernutrition PhD Student Vonaesch lab, UNIL
Jaspreet Saini Metagenomics and metatranscriptomics approach to investigate microbial communities of wastewater treatment Postdoc Holliger lab, EPFL
Nicolas Näpflin Identifying novel interesting microbes, microbial interactions and ecological patterns in the rare biosphere PhD Student Von Mering lab, University of Zurich
Margaret Vogel Predicting community assembly and stability in microbial systems Postdoc Mitri lab, UNIL
Snorre Sulheim How cross-feeding and nutrient competition shape microbial communities Postdoc Mitri lab, UNIL
Lilith Feer Curation, management and analysis of bioinformatic data and development of bioinformatic methods and tools Bioinformatician Sunagawa lab, ETHZ
Noa Barak-Gavish Investigating microbial interactions that govern bacterial phenotypic plasticity in plant microbiomes. Postdoc Vorholt lab, ETHZ
Bouke Bentvelsen Automated recognition of bacterial species using live cell imaging techniques Junior scientist van der Meer lab, UNIL
Alyssa Henderson Drivers of metabolic interactions and the structure of distributed metabolism PhD student Ackermann lab, ETHZ
Anna Weiss Elucidating the effects of functional redundancy and bacterial interaction networks on functional stability of microbial communities Postdoc Ackermann/Schubert lab, ETHZ
Elindi De Coning Gut biomarkers for Alzheimer’s Disease PhD student Bertelli lab, CHUV
Eugenio Pérez Molphe Montoya Dilucidating prokaryotic biogeographical patterns at a global scale and the biotic factors driving them. PhD student von Mering lab, UZH
Florent Mazel Ecology and evolution of the gut microbiome of social bees and rodents Senior Researcher Engel lab, UNIL
Méline Garcia Colonization success of bacteria in the gut microbiota of the western honeybee PhD student Engel lab, UNIL
Omar Keshk Genome-Scale Metabolic Models for a Synthetic Soil Microbial Community as a Path for Understanding Community Functioning PhD student Hatzimanikatis lab, EPFL
Tatiana Galperine Intestinal Microbiota Transplantation Center Senior Lecturer and MD (Infectious Diseases) Guery lab, CHUV
Jiayi Lan Non-invasive monitoring of host-microbiota metabolism with SESI-MS Technical Expert Slack lab, ETHZ
Megan Lee Determining the structure of microbial metabolic niche breadth across taxonomic hierarchy PhD student Ackermann-Schubert lab, ETHZ
Raphaël Baudin Investigating the gut phageome in Eubiosis / Using bacteriophages for the treatment of Salmonella infections Research Assistant Resch lab, CHUV
Benjamin Raach Expanding the proteome allocation framework from population to multi-species communities PhD student Ackermann-Schubert lab, ETHZ

NCCR Alumni

Karen Viacava Arsenic methylation as an emergent properties in soil microbiomes Now at Institute of Geography, University of Bern
Daniel Weilandt Large scale kinetic models of microbes Now at Princeton University, USA
François Peaudecerf The biophysics of microbial communities on leaves Now at Physics Institute, University of Rennes, France
Martin Schäfer Mapping and elucidating bacterial interactions in the plant microbiome Now at CSL Behring, Bern
Lucas Hemmerle Enrichment/Isolation and characterization of Accumulibacter using microfluidic-based approaches Now at Nestlé R&D, Lausanne
Alyson Hockenberry Synthetic microbiomes as model systems to study the dynamics of host-associated communities and analyze the basis of disease resistance Now at Loyola University Chicago
Alessio Milanese Developing new approaches for the integrated analysis of multi-omics data from microbial communities Now at DSM-Firmenich, Delft, Netherlands
Mihai Danaila Increasing scalability, modularity and performance of the Microbe Atlas Project Now at ETH Zurich
Jiangtao Qiao The emergent property of arsenic methylation in anaerobic paddy soil-derived microbiomes Now at CNRS-Université de Lorraine, France
Yassine el Chazli Elucidating host-microbial metabolic cross-talk in the gut of the western honey bee apis mellifera
Eileen Haring Functional study of protective IgA specificities induced by invasive intestinal pathogenic bacteria
Karol Piera Combining synthetic biology and microfluidics to understand dynamics of microbial interactions in space Now at DBC, University of Lausanne
Elif Esvap Constructing gut microbial community models for autism spectrum disorder through metabolic modeling Now at Bogazici University, Turkey
Ruizhe Pei Enrichment of Accumulibacter and the formation of aerobic granular sludge in wastewater treatment plants Now at University of Vienna, Austria