Bio

Assistant Professor of Microbiome Research: since 7/2016
      Institute of Microbiology, Department of Biology
      ETH Zurich, Zurich, Switzerland

Research and Staff Scientist: 2012-2016
Postdoctoral Fellow: 2010-2011
      Computational Biology (Bork Group)
      European Molecular Biology Laboratory, Heidelberg, Germany

PhD. in Quantitative and Systems Biology: 2010
      University of California, Merced, USA
MSc in Aquatic Tropical Ecology: 2005
      University of Bremen, Germany
Diploma in Biochemistry: 2002
      Johann Wolfgang Goethe-University, Frankfurt, Germany



Research
Dr. Shinichi Sunagawa's research interests revolve around environmental and host-associated microbial communities. During his MSc and PhD, he studied corals to test for differential host gene expression and microbial community changes as a response to temperature stress and disease, using a combination of field-experiments, laboratory work and bioinformatic analyses of taxonomic composition and host gene-expression data.

Selected highlights of his work in the Computational Biology Group of Dr. Peer Bork at EMBL Heidelberg include the demonstration of strain-level individuality of the human gut microbiome based on the first metagenome-wide SNP analysis, a global-scale analysis of the structure and function of the ocean microbiome, and the development of bioinformatic tools for metagenomic data mining. More recently, he co-led a study in which gut microbial strain populations were tracked after fecal microbiota transplantation in metabolic syndrome patients.

He also serves as bioinformatics coordinator for the Tara Oceans Consortium and the Tara Pacific Consortium, which aim at advancing our understanding of the ocean ecosystem at global scale. The first results of Tara Oceans were highlighted in a special issue of Science on ocean plankton and more recently, in a study of plankton-mediated carbon export in the oligotrophic ocean. For more information and media coverage, see also:
  • Features in: Science, Nature, Cell, Nature Rev Microbiol
  • On TV: ZDF - heute journal (3 min; German); SWR - Natuerlich! (4 min; German)
  • Press release: At Tara Expeditions' website
  • Press: NY Times, BBC News, Le Monde, Spiegel Online, etc...
  • Tara Oceans' science digest: in 6 min
  • Creative outreach: Science x Rhymes (YouTube)

    In July 2016, he joined ETH Zurich as an Assistant Professor of Microbiome Research at the Institute of Microbiology at the Department of Biology. His research group is interested in developing and combining bioinformatic and experimental approaches to integrate quantitative 'meta-omics' data with contextual information, with the goal to better understand and predict the role of environmental microorganisms and the driving mechanisms of host-microbial homeostasis.

  • Selected Publications (out of 70; see also: Google Scholar, Web of Science, Research Gate, PubMed)

    Human microbiome research
    Durable coexistence of donor and recipient strains after fecal microbiota transplantation
    Li SS, et al.
    Science: 352(6285), 586-589, 2016.
    Disentangling disease- and drug signatures of the human gut microbiome: the case of type 2 diabetes mellitus
    Forslund K*, Hildebrand F*, Nielsen T*, Falony G*, Le Chatelier E*, et al.
    Nature: 528(7581), 262-266, 2015.
    Genomic variation landscape of the human gut microbiome
    Schloissnig S*, Arumugam M*, Sunagawa S*, et al.
    Nature: 493(7430), 45-50, 2013.
    Enterotypes of the human gut microbiome
    Arumugam M*, Raes J*, et al.
    Nature: 473(7346), 174-180, 2011.
    Ocean ecosystems biology
    Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses
    Roux S, et al.
    Nature: 537(7622), 689-693, 2016.
    Computational eco-systems biology in Tara Oceans: translating data into knowledge
    Sunagawa S, et al.
    Mol Syst Biol: 11(5), 809, 2015.
    Structure and function of the global ocean microbiome
    Sunagawa S*#, Coelho LP*, Chaffron S*, et al.
    Science: 348(6237), 1261359, 2015.
    Patterns and ecological drivers of ocean viral communities
    Brum JR*, Ignacio-Espinoza C*, Roux S*, et al.
    Science: 348(6237), 1261498, 2015.
    Bioinformatics tools
    MOCAT2: a metagenomics assembly, annotation and profiling framework
    Kultima JR, et al.
    Bioinformatics: 32(16), 2520-2523, 2016.
    Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
    Nielsen HB*, Almeida M*, et al.
    Nature Biotechnol: 32(8), 822-828, 2014.
    Metagenomic species profiling using universal phylogenetic marker genes
    Sunagawa S, et al.
    Nature Methods: 10(12), 1196-1199, 2013.
    Accurate and universal delineation of prokaryotic species
    Mende DR, et al.
    Nature Methods: 10(9), 881-884, 2013.
    Coral-microbial symbiosis
    Threatened Corals Provide Underexplored Microbial Habitats
    Sunagawa S, et al.
    PLoS ONE: 5(3), e9554, 2010.
    Coral host transcriptomic states are correlated with Symbiodinium genotypes
    DeSalvo MK*, Sunagawa S*, et al.
    Mol Ecol: 19(6), 1174-1186, 2010.
    Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
    Sunagawa S, et al.
    ISME J: 3(5), 512-521, 2009.


    Contact

    ETH Zurich
    Institute of Microbiology, D-BIOL
    HCI F423, Vladimir-Prelog-Weg 4
    8093 Zurich
    Switzerland
    Email: ssunagawa@ethz.ch
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