Organisation

Management organigramme of the NCCR Microbiomes

Direction

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

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

Ianina Altshuler Microbiome Adaptation to the Changing Environment, EPFL Lab website

Marco Keiluweit Molecular Biogeochemistry of Soils, UNIL Lab website

Sonja Lehtinen Evolutionary Epidemiology, UNIL Lab website

The NCCR Consortium

The NCCR Microbiomes is a consortium integrating 25 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), Dr. Eavan Dorcey (Operational Manager), and Dr. Kendra Brown (Data 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

Milos Stojanov Materno-fetal and Obstetrics Research unit, CHUV Lab website

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 Postdoc 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 Postdoc 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

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

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 Postdoc Hardt lab, ETH Zurich

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

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

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 Keiluweit 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

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 PhD student Resch lab, CHUV

Benjamin Raach Expanding the proteome allocation framework from population to multi-species communities PhD student Ackermann-Schubert lab, ETHZ

Clara Heiman The role of phage tail-like particles in the establishment of plant-beneficial bacteria in the rhizosphere microbiome Postdoc Keel lab, UNIL

Prajwal Padmanabha Understanding community assembly in different environmental contexts Postdoc Mitri lab, UNIL

Xiaobing Wu Ectopic colonization by oral bacteria in the small intestine of stunted children PhD student Vonaesch lab, UNIL

Simiao Wang Microbial community dynamics during variable hydrological forcing PhD student Bernier-Latmani lab, EPFL

Isaline Guex Development of Mathematical Models for Competitive Growth, Resource Utilization and Metabolite Cross-Feeding in Complex Structured Soil (Meta)-Communities Postdoc van der Meer lab, UNIL

Elisa Romanelli Effect of flow on the marine particle microbiome Postdoc Stocker lab, ETHZ

Bruna Fornasari Investigating the presence of a pollutant on soil microbiome dynamics Junior scientist van der Meer lab, UNIL

Juan Pablo Rueda Ramirez Developing a single droplet transcriptomics approach to investigate bacterial interspecific interactions Junior scientist van der Meer lab, UNIL

Farid Chaabane Empowering the Translational Framework of Microbiota: From Software to Microbial Community Coalescence PhD student Bertelli lab, CHUV

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

Birge Özel-Duygan Tracing microbes’ fingerprints using flow cytometry data

Disha Tandon Understanding long term evolution of live vaccine bacterial species in association with gut microbiota inside mammalian gastrointestinal tract Now at University of Neuchatel

Giorgia Greter Evaluating microbial population dynamics in the gut using a 3-membered microbiota Now ETH Pioneer Fellow

Matthias Hülsmann Enhancing the productivity of the edible microalga Chlorella vulgaris by co-cultivation with designed microbial consortia Now at Pharmabiome AG

Lea Fuchs Identification of metabolic pathways relevant for gut colonization in Salmonella Typhimurium Now at Biotronik

Jiayi Lan Non-invasive monitoring of host-microbiota metabolism with SESI-MS Now at Hong Kong Science and Technology Parks Corporation

Sandra Sulser Technology Transfer Advisor Now at USZ Foundation

Carla Hernández Cabanyero Molecular mechanisms involved in the interplay of the small intestinal microbiome with inflammation and nutrient absorption Now at Ifremer, Montpellier, France