Section outline

  • Symposium + Workshop Microbiome 2018

    Villars, 10-12 & 12-14 September 2018

    This page is addressed to registered participants. To access the course description and the application form, please click here.

    For any assistance, please contact

  • Organizers: Pilar Junier, Andrea Bshary

    Monday 10.09

    9:00-10:30 Arrival, welcom, coffee

    10:30-12:00 “Strategies of metagenomic analysis” (Shinichi Sunagawa, Institute of Microbiology, ETHZ)

    12:00-14:00 Lunch break

    14:00-15:00 “The bacterial microbiome of fungi” (Geoffrey House, Los Alamos National Laboratory)

    15:00 Coffee break

    15:30-18:00 Presentations by the participants, Work in groups


    Tuesday 11.09

    7:00-8:00 running around Villars (start at the hotel lobby at 7 am);

    9:00-10:30 “Microbiota profiling in a diagnostic laboratory: quality aspects & applications” (Gilbert Greub, Institute of Microbiology, CHUV)

                      “Inferring Microbial Interactions and therapeutic effects from Metagenomic Time-series”  (Patrick Favre, Department of Biology, University of Fribourg)

    10:30-11:00 Coffee break

    11:00-12:30 “Oral microbiota in health and disease” (Vladimir Lazarevic, Genomic Research Laboratory, University of Geneva)

                        “Large scale recovery of genomes from metagenomes” (Rob Finn, European Bioinformatics Institute, Hinxton)

    12:45-14:00 Lunch break

    14:00-16:00 “Manipulating composition and functions of the plant root microbiome” (Klaus Schlaeppi, Institute of Plant Sciences, University of Bern)

                         “Effects of inoculation of cassava with genetically similar mycorrhizal fungi on local mycorrhizal fungal communities and why it matters” (Ian Sanders, Department of Ecology and Evolution, University of Lausanne)

                         “Genome recovery from environmental metagenomic datasets” (Bastiaan von Meijenfeldt, Utrecht University)

    16:00 Coffee break and outdoors activity


    Wednesday 12.09

    9:00-10:00 "The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen." (Laurent Falquet, Department of Biology, University of Fribourg)

    10:00-10:30 Coffee break

    10:30-12:30 Discussion and round tables

    12:45 Lunch

    End of the Symposium

  • Organizers: Pilar Junier, Grégoire Rossier 

    Wednesday 12.09


    • Introduction to metagenomics data analysis: why provenance matters (Alex Mitchell, EBI)
    • Markers, reference databases and genes for taxonomic analysis (Rob Finn, EBI)


    Thurdsay 13.09


    • Targeted analysis considerations and hands-on example with Mothur on Galaxy (Laurent Falquet, University of Fribourg / SIB)


    • EBI metagenomics with hands on (EBI)
    • Assembly & Binning (EBI)


    Friday 14.09


    • Bacteria within fungal genome with hands-on using EDGE platform (Geoffrey House)


    • Co-assembly and species/strain resolution
    • Tools for comparative metagenomics or Estimating sequence diversity and coverage

    End of the event: around 4 PM