Bio

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

Research and Staff Scientist: 2012-2016
Postdoctoral Fellow: 2010-2011
      Computational Biology / Microbiome Research
      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
Shinichi Sunagawa's research interests revolve around environmental and host-associated microbial communities. During his MSc and PhD, he studied reef-building corals to study host gene expression and microbial community changes in response to temperature stress and disease, using a combination of field-experiments, laboratory work and bioinformatic analyses. His thesis work showed that endangered corals provide habitats for diverse microbial communities that shift in composition in response to disease, and that microbial symbionts rather than host genotypic factors determine gene expression at the organismal level, unless the coral host is thermally stressed [1, 2, 3].

After his PhD, we worked in the Computational Biology Group of Peer Bork at the European Molecular Biology Laboratory, Germany, before he was appointed as Assistant Professor of Microbiome Research at the Department of Biology at ETH Zürich. Since 2018, he is also an associated Group Leader at the Swiss Institute of Bioinformatics. His research group is interested in 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 host-microbial interactions.

Selected highlights of his work include: the demonstration of individuality of human gut microbial strain populations based on metagenome-wide single-nucleotide variant analyses [4, 5], a global-scale analysis of the structure, function and activity of the global ocean microbiome [6, 7], and the development of bioinformatic tools for meta'omic data analysis [8, 9, 10].

He 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. For more information and media coverage, see:
  • Features in: Science, Nature, Cell, Nature Rev Microbiol
  • On TV: ZDF - heute journal (3 min; German); SWR - Natuerlich! (4 min; German)
  • Press release: by the Tara Ocean Foundation
  • Press: NY Times, BBC News, Le Monde, Spiegel Online, etc...
  • Tara Oceans' science digest: in 6 min
  • Creative outreach: Science x Rhymes (YouTube)

    Additional results on the analysis of Tara Oceans data, showing latitudinal gradients of plankton diversity [11] and geographic differences in the mechanisms of activity changes in ocean microbial communinties [7], were highlighted a recent issue of Cell. See the press release and features:
  • in scientific journals: Nature Rev Microbiol
  • in the press: Le Temps (print edition - front page)
  • on YouTube by: CellPress and ETH Zürich

  • Selected Publications (out of 90; see also: Google Scholar, Web of Science, Research Gate, PubMed)

    Ocean ecosystems biology
    Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome
    Salazar G*, Paoli L*, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, Field CM, Coelho LP, Cruaud C, Engelen S, Gregory AC, Labadie K, Marec C, Pelletier E, Royo-Llonch M, Roux S, Sanchez P, Uehara H, Zayed AA, Zeller G, Carmichael M, Dimier C, Ferland J, Kandels S, Picheral M, Pisarev S, Poulain J, Tara Oceans Coordinators, Acinas SG, Babin M, Bork P, Bowler C, de Vargas C, Guidi L, Hingamp P, Iudicone D, Karp-Boss L, Karsenti E, Ogata H, Pesant S, Speich S, Sullivan MB, Wincker P, Sunagawa S#
    Cell: 179(5), 1068-1083, 2019.
    Marine microbial diversity
    Salazar G, Sunagawa S#
    Curr Biol: 27(11), R489-R494, 2017.
    Computational eco-systems biology in Tara Oceans: translating data into knowledge
    Sunagawa S, Karsenti E, Bowler C, Bork P
    Mol Syst Biol: 11(5), 809, 2015.
    Structure and function of the global ocean microbiome
    Sunagawa S*#, Coelho LP*, Chaffron S*, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Tara Oceans Coordinators , Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P
    Science: 348(6237), 1261359, 2015.
    Gastrointestinal microbiome research
    Microbiota stability in healthy individuals after single-dose lactulose challenge - a randomized controlled study
    Wotzka SY*, Kreuzer M*, Maier L*, Zünd M*, Schlumberger M, Nguyen B, Fox M, Pohl D, Heinrich H, Rogler G, Biedermann L, Scharl M, Sunagawa S#, Hardt WD#, Misselwitz B#
    PLoS ONE: 3(10), e0206214, 2018.
    Durable coexistence of donor and recipient strains after fecal microbiota transplantation
    Li SS, Zhu A, Benes V, Costea PI, Hercog R, Hildebrand F, Huerta-Cepas J, Niewdorp M, Salojarvi J, Voigt AY, Zeller G, Sunagawa S#, de Vos WM#, Bork P#
    Science: 352(6285), 586-589, 2016.
    Genomic variation landscape of the human gut microbiome
    Schloissnig S*, Arumugam M*, Sunagawa S*, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Weinstock GM, Bork P
    Nature: 493(7430), 45-50, 2013.
    Bioinformatics tools
    Microbial abundance, activity, and population genomic profiling with mOTUs2
    Milanese A*, Mende DR*, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G#, Sunagawa S#
    Nat Commun: 10, 1014, 2019.
    Metagenomic species profiling using universal phylogenetic marker genes
    Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen OP, Guarner F, de Vos WM, Wang J, Li J, Dore J, Ehrlich SD, Stamatakis A, Bork P
    Nat Methods: 10(12), 1196-1199, 2013.
    MOCAT: a metagenomics assembly and gene prediction toolkit
    Kultima JR*, Sunagawa S*, Li J, Chen W, Chen H, Mende DR, Arumugam M, Pan Q, Liu B, Qin J, Wang J, Bork P
    PLoS ONE: 7(10), e47656, 2012.
    Coral-microbial symbiosis
    Threatened Corals Provide Underexplored Microbial Habitats
    Sunagawa S, Woodley CM, Medina M
    PLoS ONE: 5(3), e9554, 2010.
    Coral host transcriptomic states are correlated with Symbiodinium genotypes
    DeSalvo MK*, Sunagawa S*, Fisher PL, Voolstra CR, Iglesias-Prieto R, Medina M
    Mol Ecol: 19(6), 1174-1186, 2010.
    Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata
    Sunagawa S, DeSantis TZ, Piceno YM, Brodie EL, DeSalvo MK, Voolstra CR, Weil E, Andersen GL, Medina M
    ISME J: 3(5), 512-521, 2009.


    Contact

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