Bio
Associate Professor of Microbiome Research: since 10/2020
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. The Microbiome Research Laboratory he chairs at ETH Zurich 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 [1, 2], a global-scale analysis of the structure, function [3], activity [4], and biosynthetic potential [5] of the global ocean microbiome, and the development of bioinformatic tools for meta'omic data analysis [6, 7, 8].

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 [4], 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 152; see also: Google Scholar, Web of Science, Research Gate, PubMed)
    Ocean ecosystems biology
    Biosynthetic potential of the global ocean microbiome
    Paoli L, Ruscheweyh HJ, Forneris CC, Hubrich F, Kautsar S, Bhushan A, Lotti A, Clayssen Q, Salazar G, Milanese A, Carlstrom CI, Papadopoulou C, Gehrig D, Karasikov M, Mustafa H, Larralde M, Carroll LM, Sanchez P, Zayed AA, Cronin DR, Acinas SG, Bork P, Bowler C, Delmont TO, Gasol JM, Gossert AD, Kahles A, Sullivan MB, Wincker P, Zeller G, Robinson SL#, Piel J#, Sunagawa S#
    Nature: 607(7917), 111-118, 2022.
    Tara Oceans: towards global ocean ecosystems biology
    Sunagawa S#, Acinas SG, Bork P, Bowler C, Tara Oceans Coordinators, Eveillard D, Gorsky G, Guidi L, Iudicone D, Karsenti E, Lombard F, Ogata H, Pesant S, Sullivan MB, Wincker P, de Vargas C
    Nat Rev Microbiol: 18(8), 428-445, 2020.
    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.
    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
    High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains
    Zünd M, Ruscheweyh HJ, Field CM, Meyer N, Cuenca M, Hoces D, Hardt WD, Sunagawa S#
    Microbiome: 9(1), 77, 2021.
    Import of aspartate and malate by DcuABC drives H2/fumarate respiration to promote initial Salmonella gut-lumen colonization
    Nguyen BD , Cuenca M, Hartl J, Gul E, Bauer R, Meile S, Ruthi J, Margot C, Heeb L, Besser F, Perez Escriva P, Fetz C, Furter M, Laganenka L, Keller P, Fuchs LM, Christen M, Porwollik S, McClelland M, Vorholt JA, Sauer U, Sunagawa S#, Christen B#, Hardt WD#
    Cell Host Microbe: 27(6), 922-936, 2020.
    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
    Cultivation-independent genomes greatly expand taxonomic profiling capabilities of mOTUs across various environments
    Ruscheweyh HJ*, Milanese A*, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G#, Sunagawa S#
    Microbiome: 10(1), 212, 2022.
    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.
    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 Zurich
    Institute of Microbiology, D-BIOL
    HCI F417, Vladimir-Prelog-Weg 4
    8093 Zürich
    Switzerland
    Email: ssunagawa@ethz.ch
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